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Van Loy B, Stevaert A, Naesens L. The coronavirus nsp15 endoribonuclease: A puzzling protein and pertinent antiviral drug target. Antiviral Res 2024; 228:105921. [PMID: 38825019 DOI: 10.1016/j.antiviral.2024.105921] [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: 04/12/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
The SARS-CoV-2 pandemic has bolstered unprecedented research efforts to better understand the pathogenesis of coronavirus (CoV) infections and develop effective therapeutics. We here focus on non-structural protein nsp15, a hexameric component of the viral replication-transcription complex (RTC). Nsp15 possesses uridine-specific endoribonuclease (EndoU) activity for which some specific cleavage sites were recently identified in viral RNA. By preventing accumulation of viral dsRNA, EndoU helps the virus to evade RNA sensors of the innate immune response. The immune-evading property of nsp15 was firmly established in several CoV animal models and makes it a pertinent target for antiviral therapy. The search for nsp15 inhibitors typically proceeds via compound screenings and is aided by the rapidly evolving insight in the protein structure of nsp15. In this overview, we broadly cover this fascinating protein, starting with its structure, biochemical properties and functions in CoV immune evasion. Next, we summarize the reported studies in which compound screening or a more rational method was used to identify suitable leads for nsp15 inhibitor development. In this way, we hope to raise awareness on the relevance and druggability of this unique CoV protein.
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Affiliation(s)
- Benjamin Van Loy
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Annelies Stevaert
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Lieve Naesens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium.
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2
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Weller JA, Rohs R. Structure-Based Drug Design with a Deep Hierarchical Generative Model. J Chem Inf Model 2024. [PMID: 39058534 DOI: 10.1021/acs.jcim.4c01193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Recently, the remarkable growth of available crystal structure data and libraries of commercially available or readily synthesizable molecules have unlocked previously inaccessible regions of chemical space for drug development. Paired with improvements in virtual ligand screening methods, these expanded libraries are having a notable impact on early drug design efforts. Yet screening-based methods still face scalability limits, due to computational constraints and the sheer scale of drug-like space. Machine learning approaches are overcoming these limitations by learning the fundamental intra- and intermolecular relationships in drug-target systems from existing data. Here, we introduce DrugHIVE, a deep hierarchical variational autoencoder that outperforms state-of-the-art autoregressive and diffusion-based methods in both speed and performance on common generative benchmarks. DrugHIVE's hierarchical design enables improved control over molecular generation. Its capabilities include dramatically increasing virtual screening efficiency and accelerating a wide range of common drug design tasks, including de novo generation, molecular optimization, scaffold hopping, linker design, and high-throughput pattern replacement. Our highly scalable method can even be applied to receptors with high-confidence AlphaFold-predicted structures, extending the ability to generate high-quality drug-like molecules to a majority of the unsolved human proteome.
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Affiliation(s)
- Jesse A Weller
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, California 90089, United States
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3
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Gonçalves PB, Sodero ACR, Cordeiro Y. Natural products targeting amyloid-β oligomer neurotoxicity in Alzheimer's disease. Eur J Med Chem 2024; 276:116684. [PMID: 39032401 DOI: 10.1016/j.ejmech.2024.116684] [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: 06/06/2024] [Revised: 07/07/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Alzheimer's disease (AD) constitutes a major global health issue, characterized by progressive neurodegeneration and cognitive impairment, for which no curative treatment is currently available. Current therapeutic approaches are focused on symptom management, highlighting the critical need for disease-modifying therapy. The hallmark pathology of AD involves the aggregation and accumulation of amyloid-β (Aβ) peptides in the brain. Consequently, drug discovery efforts in recent decades have centered on the Aβ aggregation cascade, which includes the transition of monomeric Aβ peptides into toxic oligomers and, ultimately, mature fibrils. Historically, anti-Aβ strategies focused on the clearance of amyloid fibrils using monoclonal antibodies. However, substantial evidence has highlighted the critical role of Aβ oligomers (AβOs) in AD pathogenesis. Soluble AβOs are now recognized as more toxic than fibrils, directly contributing to synaptic impairment, neuronal damage, and the onset of AD. Targeting AβOs has emerged as a promising therapeutic approach to mitigate cognitive decline in AD. Natural products (NPs) have demonstrated promise against AβO neurotoxicity through various mechanisms, including preventing AβO formation, enhancing clearance mechanisms, or converting AβOs into non-toxic species. Understanding the mechanisms by which anti-AβO NPs operate is useful for developing disease-modifying treatments for AD. In this review, we explore the role of NPs in mitigating AβO neurotoxicity for AD drug discovery, summarizing key evidence from biophysical methods, cellular assays, and animal models. By discussing how NPs modulate AβO neurotoxicity across various experimental systems, we aim to provide valuable insights into novel therapeutic strategies targeting AβOs in AD.
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Affiliation(s)
| | | | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, 21949-900, Brazil
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Achappa S, Aldabaan NA, Desai SV, Muddapur UM, Shaikh IA, Mahnashi MH, Alshehri AA, Mannasaheb BA, Khan AA. Computational Exploration of Potential Pharmacological Inhibitors Targeting the Envelope Protein of the Kyasanur Forest Disease Virus. Pharmaceuticals (Basel) 2024; 17:884. [PMID: 39065734 PMCID: PMC11279457 DOI: 10.3390/ph17070884] [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: 05/25/2024] [Revised: 06/19/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
The limitations of the current vaccination strategy for the Kyasanur Forest Disease virus (KFDV) underscore the critical need for effective antiviral treatments, highlighting the crucial importance of exploring novel therapeutic approaches through in silico drug design. Kyasanur Forest Disease, caused by KFDV, is a tick-borne disease with a mortality of 3-5% and an annual incidence of 400 to 500 cases. In the early stage of infection, the envelope protein plays a crucial role by facilitating host-virus interactions. The objective of this research is to develop effective antivirals targeting the envelope protein to disrupt the virus-host interaction. In line with this, the 3D structure of the envelope protein was modeled and refined through molecular modeling techniques, and subsequently, ligands were designed via de novo design and pharmacophore screening, yielding 12 potential hits followed by ADMET analysis. The top five candidates underwent geometry optimization and molecular docking. Notably, compounds L4 (SA28) and L3 (CNP0247967) are predicted to have significant binding affinities of -8.91 and -7.58 kcal/mol, respectively, toward the envelope protein, based on computational models. Both compounds demonstrated stability during 200 ns molecular dynamics simulations, and the MM-GBSA binding free-energy values were -85.26 ± 4.63 kcal/mol and -66.60 ± 2.92 kcal/mol for the envelope protein L3 and L4 complexes, respectively. Based on the computational prediction, it is suggested that both compounds have potential as drug candidates for controlling host-virus interactions by targeting the envelope protein. Further validation through in-vitro assays would complement the findings of the present in silico investigations.
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Affiliation(s)
- Sharanappa Achappa
- Department of Biotechnology, KLE Technological University, Hubballi 580031, Karnataka, India; (S.A.); (U.M.M.)
| | | | - Shivalingsarj V. Desai
- Department of Biotechnology, KLE Technological University, Hubballi 580031, Karnataka, India; (S.A.); (U.M.M.)
| | - Uday M. Muddapur
- Department of Biotechnology, KLE Technological University, Hubballi 580031, Karnataka, India; (S.A.); (U.M.M.)
| | - Ibrahim Ahmed Shaikh
- Department of Pharmacology, College of Pharmacy, Najran University, Najran 66462, Saudi Arabia
| | - Mater H. Mahnashi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Najran University, Najran 66462, Saudi Arabia;
| | - Abdullateef A. Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran 66462, Saudi Arabia;
| | | | - Aejaz Abdullatif Khan
- Department of General Science, Ibn Sina National College for Medical Studies, Jeddah 21418, Saudi Arabia
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5
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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6
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Sai M, Hank EC, Tai HM, Kasch T, Lewandowski M, Vincendeau M, Marschner JA, Merk D. Development of Nurr1 agonists from amodiaquine by scaffold hopping and fragment growing. Commun Chem 2024; 7:149. [PMID: 38951694 PMCID: PMC11217349 DOI: 10.1038/s42004-024-01224-0] [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: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 07/03/2024] Open
Abstract
The neuroprotective transcription factor nuclear receptor-related 1 (Nurr1) has shown great promise as a therapeutic target in Parkinson's and Alzheimer's disease as well as multiple sclerosis but high-quality chemical tools for pharmacological target validation of Nurr1 are rare. We have employed the weak Nurr1 modulator amodiaquine (AQ) and AQ-derived fragments as templates to design a new Nurr1 agonist chemotype by scaffold hopping and fragment growing strategies. Systematic structural optimization of this scaffold yielded Nurr1 agonists with nanomolar potency and binding affinity. Comprehensive in vitro profiling revealed efficient cellular target engagement and compliance with the highest probe criteria. In human midbrain organoids bearing a Parkinson-driving LRRK2 mutation, a novel Nurr1 agonist rescued tyrosine hydroxylase expression highlighting the potential of the new Nurr1 modulator chemotype as lead and as a chemical tool for biological studies.
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Affiliation(s)
- Minh Sai
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Emily C Hank
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Hin-Man Tai
- Helmholtz Munich, Institute of Virology, 85764, Munich, Germany
| | - Till Kasch
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Max Lewandowski
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Michelle Vincendeau
- Helmholtz Munich, Institute of Virology, 85764, Munich, Germany
- Technical University of Munich, Institute of Virology, School of Medicine, 81675, Munich, Germany
| | - Julian A Marschner
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Daniel Merk
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany.
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7
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Schuh M, Boldini D, Sieber SA. Synergizing Chemical Structures and Bioassay Descriptions for Enhanced Molecular Property Prediction in Drug Discovery. J Chem Inf Model 2024; 64:4640-4650. [PMID: 38836773 PMCID: PMC11200265 DOI: 10.1021/acs.jcim.4c00765] [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: 05/02/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
The precise prediction of molecular properties can greatly accelerate the development of new drugs. However, in silico molecular property prediction approaches have been limited so far to assays for which large amounts of data are available. In this study, we develop a new computational approach leveraging both the textual description of the assay of interest and the chemical structure of target compounds. By combining these two sources of information via self-supervised learning, our tool can provide accurate predictions for assays where no measurements are available. Remarkably, our approach achieves state-of-the-art performance on the FS-Mol benchmark for zero-shot prediction, outperforming a wide variety of deep learning approaches. Additionally, we demonstrate how our tool can be used for tailoring screening libraries for the assay of interest, showing promising performance in a retrospective case study on a high-throughput screening campaign. By accelerating the early identification of active molecules in drug discovery and development, this method has the potential to streamline the identification of novel therapeutics.
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Affiliation(s)
- Maximilian
G. Schuh
- TUM School of Natural Sciences, Department
of Bioscience, Center for Functional Protein Assemblies (CPA), Technical University of Munich, 85748 Garching
bei München, Germany
| | - Davide Boldini
- TUM School of Natural Sciences, Department
of Bioscience, Center for Functional Protein Assemblies (CPA), Technical University of Munich, 85748 Garching
bei München, Germany
| | - Stephan A. Sieber
- TUM School of Natural Sciences, Department
of Bioscience, Center for Functional Protein Assemblies (CPA), Technical University of Munich, 85748 Garching
bei München, Germany
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8
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Aslan H, Renzi G, Angeli A, D'Agostino I, Ronca R, Massardi ML, Tavani C, Carradori S, Ferraroni M, Governa P, Manetti F, Carta F, Supuran CT. Benzenesulfonamide decorated dihydropyrimidin(thi)ones: carbonic anhydrase profiling and antiproliferative activity. RSC Med Chem 2024; 15:1929-1941. [PMID: 38911163 PMCID: PMC11187566 DOI: 10.1039/d4md00101j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/24/2024] [Indexed: 06/25/2024] Open
Abstract
In the last decades, carbonic anhydrases (CAs) have become the top investigated innovative pharmacological targets and, in particular, isoforms IX and XII have been widely studied due to the evidence of their overexpression in hypoxic tumors. The frantic race to find new anticancer agents places the quick preparation of large libraries of putative bioactive compounds as the basis of a successful drug discovery and development programme. In this context, multi-component and, in general, one-step reactions are becoming very popular and, among them, Biginelli's reaction gave clean and easy-to-isolate products. Thus, we synthesized a series of Biginelli's products (10-17a-b) and similar derivatives (20-21) bearing the benzenesulfonamide moiety, which is known to inhibit CA enzymes. Through the stopped-flow technique, we were able to assess their ability to inhibit the targeted CAs IX and XII in the nanomolar range with promising selectivity over the physiologically relevant isoforms I and II. Crystallography studies and docking simulations helped us to gain insight into the interaction patterns established in the enzyme-inhibitor complex. From a chemical similarity-based screening of in-house libraries of compounds, a diphenylpyrimidine (23) emerged. The surprisingly potent inhibitory activity of 23 for CAs IX and XII along with its strong antiproliferative effect on two (triple-negative breast cancer MDA-MB-231 and glioblastoma U87MG) cell lines laid the foundation for further investigation, again confirming the key role of CAs in cancer.
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Affiliation(s)
- Hakan Aslan
- Department of Chemistry, Faculty of Science and Arts, Sinop University Sinop Turkey
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
| | - Gioele Renzi
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
| | - Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
| | - Ilaria D'Agostino
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
- Department of Pharmacy, University of Pisa 56126 Pisa Italy
| | - Roberto Ronca
- Department of Molecular and Translational Medicine, University of Brescia 25123 Brescia Italy
| | - Maria Luisa Massardi
- Department of Molecular and Translational Medicine, University of Brescia 25123 Brescia Italy
| | - Camilla Tavani
- Department of Molecular and Translational Medicine, University of Brescia 25123 Brescia Italy
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara 66100 Chieti Italy
| | - Marta Ferraroni
- Department of Chemistry "Ugo Schiff", University of Florence Sesto Fiorentino Florence 50019 Italy
| | - Paolo Governa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena 53100 Siena Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena 53100 Siena Italy
| | - Fabrizio Carta
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence Sesto Fiorentino Florence 50019 Italy
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9
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Pahl A, Liu J, Patil S, Rezaei Adariani S, Schölermann B, Warmers J, Bonowski J, Koska S, Akbulut Y, Seitz C, Sievers S, Ziegler S, Waldmann H. Illuminating Dark Chemical Matter Using the Cell Painting Assay. J Med Chem 2024; 67:8862-8876. [PMID: 38687818 PMCID: PMC11181314 DOI: 10.1021/acs.jmedchem.4c00160] [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: 01/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Screening for small-molecule modulators of disease-relevant targets and phenotypes is the first step on the way to new drugs. Large compound libraries have been synthesized by academia and, particularly, pharmaceutical companies to meet the need for novel chemical entities that are as diverse as possible. Screening of these compound libraries revealed a portion of small molecules that is inactive in more than 100 different assays and was therefore termed "dark chemical matter" (DCM). Deorphanization of DCM promises to yield very selective compounds as they are expected to have less off-target effects. We employed morphological profiling using the Cell Painting assay to detect bioactive DCM. Within the DCM collection, we identified bioactive compounds and confirmed several modulators of microtubules, DNA synthesis, and pyrimidine biosynthesis. Profiling approaches are, therefore, powerful tools to probe compound collections for bioactivity in an unbiased manner and are particularly suitable for deorphanization of DCM.
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Affiliation(s)
- Axel Pahl
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jie Liu
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sohan Patil
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Soheila Rezaei Adariani
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Beate Schölermann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jens Warmers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Jana Bonowski
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sandra Koska
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Yasemin Akbulut
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Carina Seitz
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Slava Ziegler
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
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10
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Huang C, Hsu C, Chao M, Hsu K, Lin TE, Yen S, Tu H, Pan S. In silico identification of a novel Cdc2-like kinase 2 (CLK2) inhibitor in triple negative breast cancer. Protein Sci 2024; 33:e5004. [PMID: 38723164 PMCID: PMC11081522 DOI: 10.1002/pro.5004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024]
Abstract
Dysregulation of RNA splicing processes is intricately linked to tumorigenesis in various cancers, especially breast cancer. Cdc2-like kinase 2 (CLK2), an oncogenic RNA-splicing kinase pivotal in breast cancer, plays a significant role, particularly in the context of triple-negative breast cancer (TNBC), a subtype marked by substantial medical challenges due to its low survival rates. In this study, we employed a structure-based virtual screening (SBVS) method to identify potential CLK2 inhibitors with novel chemical structures for treating TNBC. Compound 670551 emerged as a novel CLK2 inhibitor with a 50% inhibitory concentration (IC50) value of 619.7 nM. Importantly, Compound 670551 exhibited high selectivity for CLK2 over other protein kinases. Functionally, this compound significantly reduced the survival and proliferation of TNBC cells. Results from a cell-based assay demonstrated that this inhibitor led to a decrease in RNA splicing proteins, such as SRSF4 and SRSF6, resulting in cell apoptosis. In summary, we identified a novel CLK2 inhibitor as a promising potential treatment for TNBC therapy.
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Affiliation(s)
- Cheng‐Chiao Huang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Division of General Surgery, Department of SurgeryTaipei Medical University HospitalTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Chia‐Ming Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Min‐Wu Chao
- School of Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- Institute of Biopharmaceutical Sciences, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- The Doctoral Program of Clinical and Experimental Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Kai‐Cheng Hsu
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
| | - Tony Eight Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shih‐Chung Yen
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen)ShenzhenGuangdongChina
| | - Huang‐Ju Tu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shiow‐Lin Pan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
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11
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Kumar M, Dubey R, Kumar Shukla P, Dayal D, Kumar Chaubey K, Tsai LW, Kumar S. Identification of small molecule inhibitors of RAD52 for breast cancer therapy: in silico approach. J Biomol Struct Dyn 2024; 42:4605-4618. [PMID: 37288783 DOI: 10.1080/07391102.2023.2220822] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
The breast cancer susceptibility gene 1/2 (BRCA1/2) are the key regulators in maintaining the genomic integrity and mutations in these genes have been associated with development of breast and ovarian cancers. Also, synthetic lethality has been shown in BRCA1/2 deficient cancers, when the RAD52 gene is silenced by shRNA or small molecules aptamers, suggesting a role for RAD52 in the breast cancers pathogenesis. Thus, to find the potential inhibitors of RAD52, a collection of 21,000 compounds from the ChemBridge screening library was screened to conduct molecular docking and molecular dynamics simulation (MD) against RAD52. Further, the results were validated by a density functional theory (DFT) analysis and using post-dynamics free energy calculations. Out of all screened molecules, the docking study revealed five compounds were found to have promising activities against RAD52. Moreover, the catalytic amino acid residues of RAD52 developed stable contacts with compound 8758 and 10593, as anticipated by DFT calculation, MD simulation, and post dynamics MM-GBSA energy calculation. It appears that compound 8758 is the best inhibitor against RAD52 followed by 10593 compared to the other top hits, in terms of the HOMO orbital energy (-1.0966 eV and -1.2136 eV) from DFT and the post dynamics binding free energy calculation (-54.71 and -52.43 Kcal/mol). Furthermore, a drug-like properties of lead molecules (8758 and 10593) were also seen via ADMET analysis. Based on our computational analysis, we hypothesize that a small molecule 8758 and 10593 possess the therapeutic potential in the management for breast cancer patients with a BRCA mutation via targeting RAD52.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mukesh Kumar
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Prakash Kumar Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Deen Dayal
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Kundan Kumar Chaubey
- Division of Research and Innovation, School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
| | - Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Sciences, Sharda School of Basic Science and Research, Sharda University, Greater Noida, Uttar Pradesh, India
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12
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Yazdani B, Sirous H, Enguita FJ, Brogi S, Wing PAC, Fassihi A. Discovery of novel direct small-molecule inhibitors targeting HIF-2α using structure-based virtual screening, molecular dynamics simulation, and MM-GBSA calculations. Mol Divers 2024; 28:1203-1224. [PMID: 37120484 DOI: 10.1007/s11030-023-10650-6] [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: 11/12/2022] [Accepted: 04/11/2023] [Indexed: 05/01/2023]
Abstract
Hypoxia-inducible factors (HIFs) are the main regulatory factors implicated in the adaptation of cancer cells to hypoxic stress, which has provoked much interest as an attractive target for the design of promising chemotherapeutic agents. Since indirect HIF inhibitors (HIFIs) lead to the occurrence of various side effects, the need of the hour is to develop direct HIFIs, physically interacting with important functional domains within the HIF protein structure. Accordingly, in the present study, it was attempted to develop an exhaustive structure-based virtual screening (VS) process coupled with molecular docking, molecular dynamic (MD) simulation, and MM-GBSA calculations for the identification of novel direct inhibitors against the HIF-2α subunit. For this purpose, a focused library of over 200,000 compounds from the NCI database was used for VS against the PAS-B domain of the target protein, HIF-2α. This domain was suggested to be a possible ligand-binding site, which is characterized by a large internal hydrophobic cavity, unique to the HIF-2α subunit. The top-ranked compounds, NSC106416, NSC217021, NSC217026, NSC215639, and NSC277811 with the best docking scores were taken up for the subsequent in silico ADME properties and PAINS filtration. The selected drug-like hits were employed for carrying out MD simulation which was followed by MM-GBSA calculations to retrieve the candidates showing the highest in silico binding affinity towards the PAS-B domain of HIF-2α. The analysis of results indicated that all molecules, except the NSC277811, fulfilled necessary drug-likeness properties. Four selected drug-like candidates, NSC106416, NSC217021, NSC217026, and NSC215639 were found to expose the stability profiles within the cavity located inside the PAS-B domain of HIF-2α over simulation time. Finally, the results of the MM-GBSA rescoring method were indicative of the highest binding affinity of NSC217026 for the binding site of the HIF-2α PAS-B domain among selected final hits. Consequently, the hit NSC217026 could serve as a promising scaffold for further optimization toward the design of direct HIF-2α inhibitors for cancer therapy.
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Affiliation(s)
- Behnaz Yazdani
- Department of Tissue Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
| | - Francisco J Enguita
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy.
| | - Peter A C Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afshin Fassihi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
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13
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Anand A, Ghosh P, Singh R, Gajanan Bajad N, Kumar A, Singh SK. Identification of potent histone deacetylase 2 (HDAC2) inhibitors through combined structure and ligand-based designs and molecular modelling approach. J Biomol Struct Dyn 2024; 42:4679-4698. [PMID: 37306006 DOI: 10.1080/07391102.2023.2222177] [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] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Histone deacetylase 2 (HDAC2) is associated with various neuropathic degenerative diseases and is considered a novel target for Alzheimer's disease (AD). Elevated levels of HDAC2 trigger excitatory neurotransmission and reduce synaptic plasticity, synaptic number, and memory formation. In the current study, we identified HDAC2 inhibitors using an integrated structure and ligand-based approaches to drug design. Three pharmacophore models were generated by using different pharmacophoric features and validated using the Enrichment factor (EF), Güner-henry (GH) score, and percentage yield. The model of choice was used to screen a library of Zinc-15 compounds and interfering compounds were eliminated by using drug likeliness and PAINS filtering. Further, docking studies in three stages were carried out to obtain hits with good binding energies and were followed by ADMET studies yielding three virtual hits. The virtual hits, i.e. ZINC000008184553, ZINC0000013641114, and ZINC000032533141, were subjected to molecular dynamics simulation studies. Compound ZINC000008184553, identified as lead, was found to have optimal stability, low toxicity under simulated conditions, and may potentially inhibit HDAC2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asha Anand
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Powsali Ghosh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Nilesh Gajanan Bajad
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U), Varanasi, India
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14
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Fotsch C, Basu D, Case R, Chen Q, Koneru PC, Lo MC, Ngo R, Sharma P, Vaish A, Yi X, Zech SG, Hodder P. Creating a more strategic small molecule biophysical hit characterization workflow. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100159. [PMID: 38723666 DOI: 10.1016/j.slasd.2024.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/16/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024]
Abstract
To confirm target engagement of hits from our high-throughput screening efforts, we ran biophysical assays on several hundreds of hits from 15 different high-throughput screening campaigns. Analyzing the biophysical assay results from these screening campaigns led us to conclude that we could be more strategic in our biophysical analysis of hits by first confirming activity in a thermal shift assay (TSA) and then confirming activity in either a surface plasmon resonance (SPR) assay or a temperature-related intensity change (TRIC) assay. To understand how this new workflow shapes the quality of the final hits, we compared TSA/SPR or TSA/TRIC confirmed and unconfirmed hits to one another using four measures of compound quality: quantitative estimate of drug-likeness (QED), Pan-Assay Interference Compounds (PAINS), promiscuity, and aqueous solubility. In general, we found that the biophysically confirmed hits performed better in the compound quality metrics than the unconfirmed hits, demonstrating that our workflow not only confirmed target engagement of the hits but also enriched for higher quality hits.
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Affiliation(s)
- Christopher Fotsch
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA.
| | - Debaleena Basu
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Ryan Case
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Qing Chen
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Pratibha C Koneru
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Mei-Chu Lo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Rachel Ngo
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Pooja Sharma
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Amit Vaish
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Xiang Yi
- Lead Discovery and Characterization Group, Amgen Research, South San Francisco CA, USA
| | - Stephan G Zech
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
| | - Peter Hodder
- Lead Discovery and Characterization Group, Amgen Research, Thousand Oaks CA, USA
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15
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Pidany F, Kroustkova J, Jenco J, Breiterova KH, Muckova L, Novakova L, Kunes J, Fibigar J, Kucera T, Novak M, Sorf A, Hrabinova M, Pulkrabkova L, Janousek J, Soukup O, Jun D, Korabecny J, Cahlikova L. Carltonine-derived compounds for targeted butyrylcholinesterase inhibition. RSC Med Chem 2024; 15:1601-1625. [PMID: 38784455 PMCID: PMC11110763 DOI: 10.1039/d4md00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/16/2024] [Indexed: 05/25/2024] Open
Abstract
The investigation into human butyrylcholinesterase (hBChE) inhibitors as therapeutic agents for Alzheimer's disease (AD) holds significant promise, addressing both symptomatic relief and disease progression. In the pursuit of novel drug candidates with a selective BChE inhibition pattern, we focused on naturally occurring template structures, specifically Amaryllidaceae alkaloids of the carltonine-type. Herein, we explored a series of compounds implementing an innovative chemical scaffold built on the 3- and 4-benzyloxy-benzylamino chemotype. Notably, compounds 28 (hBChE IC50 = 0.171 ± 0.063 μM) and 33 (hBChE IC50 = 0.167 ± 0.018 μM) emerged as top-ranked hBChE inhibitors. In silico simulations elucidated the binding modes of these compounds within hBChE. CNS availability was predicted using the BBB score algorithm, corroborated by in vitro permeability assessments with the most potent derivatives. Compound 33 was also inspected for aqueous solubility, microsomal and plasma stability. Chemoinformatics analysis validated these hBChE inhibitors for oral administration, indicating favorable gastrointestinal absorption in compliance with Lipinski's and Veber's rules. Safety assessments, crucial for the chronic administration typical in AD treatment, were conducted through cytotoxicity testing on human neuroblastoma (SH-SY5Y) and hepatocellular carcinoma (HepG2) cell lines.
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Affiliation(s)
- Filip Pidany
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacognosy and Pharmaceutical Botany, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Jana Kroustkova
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacognosy and Pharmaceutical Botany, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Jaroslav Jenco
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacognosy and Pharmaceutical Botany, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Katerina Hradiska Breiterova
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacognosy and Pharmaceutical Botany, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Lubica Muckova
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Lucie Novakova
- Faculty of Pharmacy in Hradec Kralove, Department of Analytical Chemistry, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Jiri Kunes
- Faculty of Pharmacy in Hradec Kralove, Department of Bioorganic and Organic Chemistry, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
| | - Jakub Fibigar
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Tomas Kucera
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Martin Novak
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
| | - Ales Sorf
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Martina Hrabinova
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Lenka Pulkrabkova
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Jiri Janousek
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Daniel Jun
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove Sokolska 581 500 05 Hradec Kralove Czech Republic
- Military Faculty of Medicine, Department of Toxicology and Military Pharmacy, University of Defence Trebesska 1575 500 01 Hradec Kralove Czech Republic
| | - Lucie Cahlikova
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacognosy and Pharmaceutical Botany, Charles University Akademika Heyrovskeho 1203 500 05 Hradec Kralove Czech Republic
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16
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Rask GC, Taslim C, Bayanjargal A, Cannon MV, Selich-Anderson J, Crow JC, Duncan A, Theisen ER. Seclidemstat blocks the transcriptional function of multiple FET-fusion oncoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.19.594897. [PMID: 38826330 PMCID: PMC11142045 DOI: 10.1101/2024.05.19.594897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Genes encoding the RNA-binding proteins FUS, EWSR1, and TAF15 (FET proteins) are involved in chromosomal translocations in rare sarcomas. FET-rearranged sarcomas are often aggressive malignancies affecting patients of all ages. New therapies are needed. These translocations fuse the 5' portion of the FET gene with a 3' partner gene encoding a transcription factor (TF). The resulting fusion proteins are oncogenic TFs with a FET protein low complexity domain (LCD) and a DNA binding domain. FET fusion proteins have proven stubbornly difficult to target directly and promising strategies target critical co-regulators. One candidate is lysine specific demethylase 1 (LSD1). LSD1 is recruited by multiple FET fusions, including EWSR1::FLI1. LSD1 promotes EWSR1::FLI1 activity and treatment with the noncompetitive inhibitor SP-2509 blocks EWSR1::FLI1 transcriptional function. A similar molecule, seclidemstat (SP-2577), is currently in clinical trials for FET-rearranged sarcomas (NCT03600649). However, whether seclidemstat has pharmacological activity against FET fusions has not been demonstrated. Here, we evaluate the in vitro potency of seclidemstat against multiple FET-rearranged sarcoma cell lines, including Ewing sarcoma, desmoplastic small round cell tumor, clear cell sarcoma, and myxoid liposarcoma. We also define the transcriptomic effects of seclidemstat treatment and evaluated the activity of seclidemstat against FET fusion transcriptional regulation. Seclidemstat showed potent activity in cell viability assays across FET-rearranged sarcomas and disrupted the transcriptional function of all tested fusions. Though epigenetic and targeted inhibitors are unlikely to be effective as a single agents in the clinic, these data suggest seclidemstat remains a promising new treatment strategy for patients with FET-rearranged sarcomas.
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Affiliation(s)
- Galen C. Rask
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Cenny Taslim
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Ariunaa Bayanjargal
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Medical Scientist Training Program, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Matthew V. Cannon
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Julia Selich-Anderson
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | - Jesse C. Crow
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
| | | | - Emily R. Theisen
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, 43215, USA
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
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17
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Zheng L, Zhang Y, Mei S, Xie T, Zou Y, Wang Y, Jing H, Xu S, Dramou P, Xu Z, Li J, Zhou Y, Niu MM. Discovery of a Potent Dual Son of Sevenless 1 (SOS1) and Epidermal Growth Factor Receptor (EGFR) Inhibitor for the Treatment of Prostate Cancer. J Med Chem 2024; 67:7130-7145. [PMID: 38630077 DOI: 10.1021/acs.jmedchem.3c02433] [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: 07/31/2024]
Abstract
Multitarget medications represent an appealing therapy against the disease with multifactorial abnormalities─cancer. Therefore, simultaneously targeting son of sevenless 1 (SOS1) and epidermal growth factor receptor (EGFR), two aberrantly expressed proteins crucial for the oncogenesis and progression of prostate cancer, may achieve active antitumor effects. Here, we discovered dual SOS1/EGFR-targeting compounds via pharmacophore-based docking screening. The most prominent compound SE-9 exhibited nanomolar inhibition activity against both SOS1 and EGFR and efficiently suppressed the phosphorylation of ERK and AKT in prostate cancer cells PC-3. Cellular assays also revealed that SE-9 displayed strong antiproliferative activities through diverse mechanisms, such as induction of cell apoptosis and G1 phase cell cycle arrest, as well as reduction of angiogenesis and migration. Further in vivo findings showed that SE-9 potently inhibited tumor growth in PC-3 xenografts without obvious toxicity. Overall, SE-9 is a novel dual-targeting SOS1/EGFR inhibitor that represents a promising treatment strategy for prostate cancer.
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Affiliation(s)
- Lufeng Zheng
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Yuxin Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Shuang Mei
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
| | - Tianyuan Xie
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Yunting Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
| | - Yuting Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Han Jing
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing 211198, China
| | - Shengtao Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Pierre Dramou
- Department of Analytical Chemistry, School of Sciences, China Pharmaceutical University, Nanjing 210009, China
| | - Zhen Xu
- Department of Pharmacy, Taizhou School of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Jindong Li
- Taizhou School of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou 225300, China
| | - Yang Zhou
- Department of Pathology, The Affiliated Changzhou Second People's Hospital of Nanjing Medical University, Changzhou 213000, China
| | - Miao-Miao Niu
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 211198, China
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18
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Zhou Y, Phelps GA, Mangrum MM, McLeish J, Phillips EK, Lou J, Ancajas CF, Rybak JM, Oelkers PM, Lee RE, Best MD, Reynolds TB. The small molecule CBR-5884 inhibits the Candida albicans phosphatidylserine synthase. mBio 2024; 15:e0063324. [PMID: 38587428 PMCID: PMC11077991 DOI: 10.1128/mbio.00633-24] [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: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Systemic infections by Candida spp. are associated with high mortality rates, partly due to limitations in current antifungals, highlighting the need for novel drugs and drug targets. The fungal phosphatidylserine synthase, Cho1, from Candida albicans is a logical antifungal drug target due to its importance in virulence, absence in the host, and conservation among fungal pathogens. Inhibitors of Cho1 could serve as lead compounds for drug development, so we developed a target-based screen for inhibitors of purified Cho1. This enzyme condenses serine and cytidyldiphosphate-diacylglycerol (CDP-DAG) into phosphatidylserine (PS) and releases cytidylmonophosphate (CMP). Accordingly, we developed an in vitro nucleotidase-coupled malachite-green-based high throughput assay for purified C. albicans Cho1 that monitors CMP production as a proxy for PS synthesis. Over 7,300 molecules curated from repurposing chemical libraries were interrogated in primary and dose-responsivity assays using this platform. The screen had a promising average Z' score of ~0.8, and seven compounds were identified that inhibit Cho1. Three of these, ebselen, LOC14, and CBR-5884, exhibited antifungal effects against C. albicans cells, with fungicidal inhibition by ebselen and fungistatic inhibition by LOC14 and CBR-5884. Only CBR-5884 showed evidence of disrupting in vivo Cho1 function by inducing phenotypes consistent with the cho1∆∆ mutant, including a reduction of cellular PS levels. Kinetics curves and computational docking indicate that CBR-5884 competes with serine for binding to Cho1 with a Ki of 1,550 ± 245.6 nM. Thus, this compound has the potential for development into an antifungal compound. IMPORTANCE Fungal phosphatidylserine synthase (Cho1) is a logical antifungal target due to its crucial role in the virulence and viability of various fungal pathogens, and since it is absent in humans, drugs targeted at Cho1 are less likely to cause toxicity in patients. Using fungal Cho1 as a model, there have been two unsuccessful attempts to discover inhibitors for Cho1 homologs in whole-cell screens prior to this study. The compounds identified in these attempts do not act directly on the protein, resulting in the absence of known Cho1 inhibitors. The significance of our research is that we developed a high-throughput target-based assay and identified the first Cho1 inhibitor, CBR-5884, which acts both on the purified protein and its function in the cell. This molecule acts as a competitive inhibitor with a Ki value of 1,550 ± 245.6 nM and, thus, has the potential for development into a new class of antifungals targeting PS synthase.
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Affiliation(s)
- Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Gregory A. Phelps
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
- Graduate School of Biomedical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mikayla M. Mangrum
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jemma McLeish
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Elise K. Phillips
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jinchao Lou
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Jeffrey M. Rybak
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Peter M. Oelkers
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan, USA
| | - Richard E. Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Michael D. Best
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
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19
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Luginina AP, Khnykin AN, Khorn PA, Moiseeva OV, Safronova NA, Pospelov VA, Dashevskii DE, Belousov AS, Borschevskiy VI, Mishin AV. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: Ligand Search and Screening. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:958-972. [PMID: 38880655 DOI: 10.1134/s0006297924050158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 06/18/2024]
Abstract
G protein-coupled receptors (GPCRs) are transmembrane proteins that participate in many physiological processes and represent major pharmacological targets. Recent advances in structural biology of GPCRs have enabled the development of drugs based on the receptor structure (structure-based drug design, SBDD). SBDD utilizes information about the receptor-ligand complex to search for suitable compounds, thus expanding the chemical space of possible receptor ligands without the need for experimental screening. The review describes the use of structure-based virtual screening (SBVS) for GPCR ligands and approaches for the functional testing of potential drug compounds, as well as discusses recent advances and successful examples in the application of SBDD for the identification of GPCR ligands.
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Affiliation(s)
- Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Valentin I Borschevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Moscow Region, 141980, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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20
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Bosch B, DeJesus MA, Schnappinger D, Rock JM. Weak links: Advancing target-based drug discovery by identifying the most vulnerable targets. Ann N Y Acad Sci 2024; 1535:10-19. [PMID: 38595325 DOI: 10.1111/nyas.15139] [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: 04/11/2024]
Abstract
Mycobacterium tuberculosis remains the most common infectious killer worldwide despite decades of antitubercular drug development. Effectively controlling the tuberculosis (TB) pandemic will require innovation in drug discovery. In this review, we provide a brief overview of the two main approaches to discovering new TB drugs-phenotypic screens and target-based drug discovery-and outline some of the limitations of each method. We then explore recent advances in genetic tools that aim to overcome some of these limitations. In particular, we highlight a novel metric to prioritize essential targets, termed vulnerability. Stratifying targets based on their vulnerability presents new opportunities for future target-based drug discovery campaigns.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
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21
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Tan L, Hirte S, Palmacci V, Stork C, Kirchmair J. Tackling assay interference associated with small molecules. Nat Rev Chem 2024; 8:319-339. [PMID: 38622244 DOI: 10.1038/s41570-024-00593-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Biochemical and cell-based assays are essential to discovering and optimizing efficacious and safe drugs, agrochemicals and cosmetics. However, false assay readouts stemming from colloidal aggregation, chemical reactivity, chelation, light signal attenuation and emission, membrane disruption, and other interference mechanisms remain a considerable challenge in screening synthetic compounds and natural products. To address assay interference, a range of powerful experimental approaches are available and in silico methods are now gaining traction. This Review begins with an overview of the scope and limitations of experimental approaches for tackling assay interference. It then focuses on theoretical methods, discusses strategies for their integration with experimental approaches, and provides recommendations for best practices. The Review closes with a summary of the critical facts and an outlook on potential future developments.
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Affiliation(s)
- Lu Tan
- Drug Discovery Sciences, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Steffen Hirte
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Vincenzo Palmacci
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences (PhaNuSpo), University of Vienna, Vienna, Austria
| | - Conrad Stork
- Department of Informatics, Center for Bioinformatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
- BASF SE, Ludwigshafen am Rhein, Germany
| | - Johannes Kirchmair
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
- Christian Doppler Laboratory for Molecular Informatics in the Biosciences, Department for Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
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22
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Boldini D, Friedrich L, Kuhn D, Sieber SA. Machine Learning Assisted Hit Prioritization for High Throughput Screening in Drug Discovery. ACS CENTRAL SCIENCE 2024; 10:823-832. [PMID: 38680560 PMCID: PMC11046457 DOI: 10.1021/acscentsci.3c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 05/01/2024]
Abstract
Efficient prioritization of bioactive compounds from high throughput screening campaigns is a fundamental challenge for accelerating drug development efforts. In this study, we present the first data-driven approach to simultaneously detect assay interferents and prioritize true bioactive compounds. By analyzing the learning dynamics during training of a gradient boosting model on noisy high throughput screening data using a novel formulation of sample influence, we are able to distinguish between compounds exhibiting the desired biological response and those producing assay artifacts. Therefore, our method enables false positive and true positive detection without relying on prior screens or assay interference mechanisms, making it applicable to any high throughput screening campaign. We demonstrate that our approach consistently excludes assay interferents with different mechanisms and prioritizes biologically relevant compounds more efficiently than all tested baselines, including a retrospective case study simulating its use in a real drug discovery campaign. Finally, our tool is extremely computationally efficient, requiring less than 30 s per assay on low-resource hardware. As such, our findings show that our method is an ideal addition to existing false positive detection tools and can be used to guide further pharmacological optimization after high throughput screening campaigns.
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Affiliation(s)
- Davide Boldini
- TUM
School of Natural Sciences, Department of Bioscience, Center for Functional
Protein Assemblies (CPA), Technical University
of Munich, 85748 Garching bei München, Germany
| | - Lukas Friedrich
- The
Healthcare business of Merck KGaA, 64293 Darmstadt, Germany
| | - Daniel Kuhn
- The
Healthcare business of Merck KGaA, 64293 Darmstadt, Germany
| | - Stephan A. Sieber
- TUM
School of Natural Sciences, Department of Bioscience, Center for Functional
Protein Assemblies (CPA), Technical University
of Munich, 85748 Garching bei München, Germany
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23
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Mahjour BA, Coley CW. RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries. J Chem Inf Model 2024; 64:2948-2954. [PMID: 38488634 DOI: 10.1021/acs.jcim.4c00138] [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: 04/23/2024]
Abstract
SMARTS is a widely used language in cheminformatics for defining substructural queries for database lookups, reaction templates for chemical transformations, and other applications. As an extension to SMILES, many SMARTS patterns can represent the same query. Despite this, no canonicalization algorithm invariant of the line notation sequence or atomic numbering is publicly available. Here, we introduce RDCanon, an open-source Python package that can be used to standardize SMARTS queries. RDCanon is designed to ensure that the sequence of atomic queries remains consistent for all graphs representing the same substructure query and to ensure a canonical sequence of primitives within each individual atom query; furthermore, the algorithm can be applied to canonicalize the order of reactants, agents, and products and their atom map numbers in reaction SMARTS templates. As part of its canonicalization algorithm, RDCanon provides a mechanism in which the canonicalized SMARTS is optimized for speed against specific molecular databases. Several case studies are provided to showcase improved efficiency in substructure matching and retrosynthetic analysis.
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Affiliation(s)
- Babak A Mahjour
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Wang L, Kumar R, Winblad B, Pavlov PF. Structure-based discovery of small molecule inhibitors of FKBP51-Hsp90 protein-protein interaction. Eur J Med Chem 2024; 270:116356. [PMID: 38579621 DOI: 10.1016/j.ejmech.2024.116356] [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: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024]
Abstract
The heat shock protein 90 kDa (Hsp90) molecular chaperone machinery is responsible for the folding and activation of hundreds of important clients such as kinases, steroid hormone receptors, transcription factors, etc. This process is dynamically regulated in an ATP-dependent manner by Hsp90 co-chaperones including a group of tetratricopeptide (TPR) motif proteins that bind to the C-terminus of Hsp90. Among these TPR containing co-chaperones, FK506-binding protein 51 kDa (FKBP51) is reported to play an important role in stress-related pathologies, psychiatric disorders, Alzheimer's disease, and cancer, making FKBP51-Hsp90 interaction a potential therapeutic target. In this study, we report identification of potent and selective inhibitors of FKBP51-Hsp90 protein-protein interaction using a structure-based virtual screening approach. Upon in vitro evaluation, the identified hits show a considerable degree of selectivity towards FKBP51 over other TPR proteins, particularly for highly homologous FKBP52. Tyr355 of FKBP51 emerged as an important contributor to inhibitor's specificity. Additionally, we demonstrate the impact of these inhibitors on cellular energy metabolism, and neurite outgrowth, which are subjects of FKBP51 regulation. Overall, the results from this study highlight a novel pharmacological approach towards regulation of FKBP51 function and more generally, Hsp90 function via its interaction with TPR co-chaperones.
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Affiliation(s)
- Lisha Wang
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden.
| | - Rajnish Kumar
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), 221005, Varanasi, India.
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Theme Inflammation and Aging, Karolinska University Hospital, 14186, Huddinge, Sweden
| | - Pavel F Pavlov
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden
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25
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Manson DE, Ananiev GE, Guo S, Ericksen SS, Santa EE, Blackwell HE. Abiotic Small Molecule Inhibitors and Activators of the LasR Quorum Sensing Receptor in Pseudomonas aeruginosa with Potencies Comparable or Surpassing N-Acyl Homoserine Lactones. ACS Infect Dis 2024; 10:1212-1221. [PMID: 38506163 PMCID: PMC11014758 DOI: 10.1021/acsinfecdis.3c00593] [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] [Indexed: 03/21/2024]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa controls almost 10% of its genome, including myriad virulence genes, via a cell-to-cell chemical communication system called quorum sensing (QS). Small molecules that either inhibit or activate QS in P. aeruginosa represent useful research tools to study the role of this signaling pathway in infection and interrogate its viability as an antivirulence target. However, despite active research in this area over the past 20+ years, there are relatively few synthetic compounds known to strongly inhibit or activate QS in P. aeruginosa. Most reported QS modulators in this pathogen are of low potency or have structural liabilities that limit their application in biologically relevant environments such as mimics of the native N-acyl l-homoserine lactone (AHL) signals. Here, we report the results of a high-throughput screen for abiotic small molecules that target LasR, a key QS regulator in P. aeruginosa. We screened a 25,000-compound library and discovered four new structural classes of abiotic LasR modulators. These compounds include antagonists that surpass the potency of all known AHL-type compounds and mimetics thereof, along with an agonist with potency approaching that of LasR's native ligand. The novel structures of this compound set, along with their anticipated robust physicochemical profiles, underscore their potential value as probe molecules to interrogate the roles of QS in this formidable pathogen.
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Affiliation(s)
- Daniel E Manson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Gene E Ananiev
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Song Guo
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Spencer S Ericksen
- Small Molecule Screening Facility, University of Wisconsin Carbone Cancer Center, 600 Highland Ave., Madison, Wisconsin 53792, United States
| | - Emma E Santa
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
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26
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Devi B, Jangid K, Kumar N, Kumar V, Kumar V. Identification of potential JNK3 inhibitors through virtual screening, molecular docking and molecular dynamics simulation as therapeutics for Alzheimer's disease. Mol Divers 2024:10.1007/s11030-024-10820-0. [PMID: 38573427 DOI: 10.1007/s11030-024-10820-0] [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: 12/13/2023] [Accepted: 01/30/2024] [Indexed: 04/05/2024]
Abstract
Alzheimer's disease (AD) is a complex neurological disorder and no effective drug is available for its treatment. Numerous pathological conditions are believed to be responsible for the initiation and development of AD including c-Jun N-terminal kinases (JNKs). The JNKs are one of the enzymes from the mitogen-activated protein kinase (MAPK) family that controls the phosphorylation of various transcription factors on serine and threonine residues, and hold significant responsibilities in tasks like gene expression, cell proliferation, differentiation, and apoptosis. Since, JNK3 is primarily expressed in the brain hence its increased levels in the brain are associated with the AD pathology promoting neurofibrillary tangles, senile plaques, neuroinflammation, and nerve cell apoptosis. The current research work is focused on the development of novel JNK inhibitors as therapeutics for AD employing a structure-based virtual screening (SBVS) approach. The ZINC database (14634052 compounds) was investigated after employing pan assay interference (PAINs), drug-likeness, and diversity picking filter to distinguish molecules interacting with JNK3 by following three docking precision criteria: High Throughput Virtual Screening (HTVS), Standard Precision (SP), and Extra Precision (XP) & MMGBSA. Five lead molecules showed a better docking score in the range of -13.091 to -14.051 kcal/mol better than the reference compound (- 11.828 kcal/mol). The lead compounds displayed acceptable pharmacokinetic properties and were subjected to molecular dynamic simulations of 100 ns and binding free energy calculations. All the lead molecules showed stable RMSD and hydrogen bond interactions throughout the trajectory. The ∆GMM/PBSA_total score for the lead compounds ZINC220382956, ZINC147071339, ZINC207081127, ZINC205151456, ZINC1228819126, and CC-930 was calculated and found to be - 31.39, - 42.8, - 37.04, - 39.01, - 36.5, - 34.16 kcal/mol, respectively. Thus, it was concluded that the lead molecules identified in these studies have the potential to be explored as potent JNK3 inhibitors.
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Affiliation(s)
- Bharti Devi
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Ghudda, 151401, India
| | - Kailash Jangid
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry and Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Ghudda, 151401, India
| | - Naveen Kumar
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Ghudda, 151401, India
| | - Vinay Kumar
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Ghudda, 151401, India
| | - Vinod Kumar
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Ghudda, 151401, India.
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27
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Chen H, Fang G, Ren Y, Zou W, Ying K, Yang Z, Chen Q. Super-resolution imaging for in situ monitoring sub-cellular micro-dynamics of small molecule drug. Acta Pharm Sin B 2024; 14:1864-1877. [PMID: 38572114 PMCID: PMC10985125 DOI: 10.1016/j.apsb.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 04/05/2024] Open
Abstract
Small molecule drugs play a pivotal role in the arsenal of anticancer pharmacological agents. Nonetheless, their small size poses a challenge when directly visualizing their localization, distribution, mechanism of action (MOA), and target engagement at the subcellular level in real time. We propose a strategy for developing triple-functioning drug beacons that seamlessly integrate therapeutically relevant bioactivity, precise subcellular localization, and direct visualization capabilities within a single molecular entity. As a proof of concept, we have meticulously designed and constructed a boronic acid fluorescence drug beacon using coumarin-hemicyanine (CHB). Our CHB design includes three pivotal features: a boronic acid moiety that binds both adenosine triphosphate (ATP) and adenosine diphosphate (ADP), thus depleting their levels and disrupting the energy supply within mitochondria; a positively charged component that targets the drug beacon to mitochondria; and a sizeable conjugated luminophore that emits fluorescence, facilitating the application of structured illumination microscopy (SIM). Our study indicates the exceptional responsiveness of our proof-of-concept drug beacon to ADP and ATP, its efficacy in inhibiting tumor growth, and its ability to facilitate the tracking of ADP and ATP distribution around the mitochondrial cristae. Furthermore, our investigation reveals that the micro-dynamics of CHB induce mitochondrial dysfunction by causing damage to the mitochondrial cristae and mitochondrial DNA. Altogether, our findings highlight the potential of SIM in conjunction with visual drug design as a potent tool for monitoring the in situ MOA of small molecule anticancer compounds. This approach represents a crucial advancement in addressing a current challenge within the field of small molecule drug discovery and validation.
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Affiliation(s)
- Huimin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Guiqian Fang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Youxiao Ren
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
| | - Kang Ying
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Qixin Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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28
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França TC, Saïdi F, Ajamian A, Islam ST, LaPlante SR. Molecular Dynamics of Outer Membrane-Embedded Polysaccharide Secretion Porins Reveals Closed Resting-State Surface Gates Targetable by Virtual Fragment Screening for Drug Hotspot Identification. ACS OMEGA 2024; 9:13217-13226. [PMID: 38524450 PMCID: PMC10955716 DOI: 10.1021/acsomega.3c09970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/06/2024] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Recent advances in iterative neural network analyses (e.g., AlphaFold2 and RoseTTA fold) have been revolutionary for protein 3D structure prediction, especially for difficult-to-manipulate α-helical/β-barrel integral membrane proteins. These model structures are calculated based on the coevolution of amino acids within the protein of interest and similarities to existing protein structures; the local effects of the membrane on folding and stability of the calculated model structures are not considered. We recently reported the discovery, 3D modeling, and characterization of 18-β-stranded outer-membrane (OM) WzpX, WzpS, and WzpB β-barrel secretion porins for the exopolysaccharide (EPS), major spore coat polysaccharide (MASC), and biosurfactant polysaccharide (BPS) pathways (respectively) in the Gram-negative social predatory bacterium Myxococcus xanthus DZ2. However, information was not obtained regarding the dynamic behavior of surface-gating WzpX/S/B loop domains or on potential treatments to inactivate these porins. Herein, we developed a molecular dynamics (MD) protocol to study the core stability and loop dynamism of neural network-based integral membrane protein structure models embedded in an asymmetric OM bilayer, using the M. xanthus WzpX, WzpS, and WzpB proteins as test candidates. This was accomplished through integration of the CHARMM-graphical user interface (GUI) and Molecular Operating Environment (MOE) workflows to allow for a rapid simulation system setup and facilitate data analysis. In addition to serving as a method of model structure validation, our molecular dynamics simulations revealed a minimal movement of extracellular WzpX/S/B loops in the absence of an external stimulus as well as druggable cavities between the loops. Virtual screening of a commercial fragment library against these cavities revealed putative fragment-binding hotspots on the cell-surface face of each β-barrel, along with key interacting residues, and identified promising hits for the design of potential binders capable of plugging the β-barrels and inhibiting polysaccharide secretion.
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Affiliation(s)
- Tanos
C. C. França
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
- Laboratory
of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro 22290-270, Brazil
- Department
of Chemistry, Faculty of Science, University
of Hradec Kralove, Rokitanskeho
62, 50003 Hradec
Kralove, Czech Republic
| | - Fares Saïdi
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Alain Ajamian
- Chemical
Computing Group, Montreal, Quebec H3A 2R7, Canada
| | - Salim T. Islam
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Steven R. LaPlante
- Institut
National de la Recherche Scientifique (INRS), Centre Armand-Frappier
Santé Biotechnologie, Université
du Québec, Institut Pasteur International Network, Laval, QC H7V 1B7, Canada
- PROTEO,
the Quebec Network for Research on Protein Function, Engineering,
and Applications, Université Laval, Quebec, QC G1V 0A6, Canada
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29
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Weller JA, Rohs R. DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573155. [PMID: 38187658 PMCID: PMC10769420 DOI: 10.1101/2023.12.22.573155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Rapid advancement in the computational methods of structure-based drug design has led to their widespread adoption as key tools in the early drug development process. Recently, the remarkable growth of available crystal structure data and libraries of commercially available or readily synthesizable molecules have unlocked previously inaccessible regions of chemical space for drug development. Paired with improvements in virtual ligand screening methods, these expanded libraries are having a significant impact on the success of early drug design efforts. However, screening-based methods are limited in their scalability due to computational limits and the sheer scale of drug-like space. An approach within the quickly evolving field of artificial intelligence (AI), deep generative modeling, is extending the reach of molecular design beyond classical methods by learning the fundamental intra- and inter-molecular relationships in drug-target systems from existing data. In this work we introduce DrugHIVE, a deep hierarchical structure-based generative model that enables fine-grained control over molecular generation. Our model outperforms state of the art autoregressive and diffusion-based methods on common benchmarks and in speed of generation. Here, we demonstrate DrugHIVEs capacity to accelerate a wide range of common drug design tasks such as de novo generation, molecular optimization, scaffold hopping, linker design, and high throughput pattern replacement. Our method is highly scalable and can be applied to high confidence AlphaFold predicted receptors, extending our ability to generate high quality drug-like molecules to a majority of the unsolved human proteome.
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30
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Rak M, Menge A, Tesch R, Berger LM, Balourdas DI, Shevchenko E, Krämer A, Elson L, Berger BT, Abdi I, Wahl LM, Poso A, Kaiser A, Hanke T, Kronenberger T, Joerger AC, Müller S, Knapp S. Development of Selective Pyrido[2,3- d]pyrimidin-7(8 H)-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. J Med Chem 2024; 67:3813-3842. [PMID: 38422480 DOI: 10.1021/acs.jmedchem.3c02217] [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: 03/02/2024]
Abstract
Mammalian STE20-like (MST) kinases 1-4 play key roles in regulating the Hippo and autophagy pathways, and their dysregulation has been implicated in cancer development. In contrast to the well-studied MST1/2, the roles of MST3/4 are less clear, in part due to the lack of potent and selective inhibitors. Here, we re-evaluated literature compounds, and used structure-guided design to optimize the p21-activated kinase (PAK) inhibitor G-5555 (8) to selectively target MST3/4. These efforts resulted in the development of MR24 (24) and MR30 (27) with good kinome-wide selectivity and high cellular potency. The distinct cellular functions of closely related MST kinases can now be elucidated with subfamily-selective chemical tool compounds using a combination of the MST1/2 inhibitor PF-06447475 (2) and the two MST3/4 inhibitors developed. We found that MST3/4-selective inhibition caused a cell-cycle arrest in the G1 phase, whereas MST1/2 inhibition resulted in accumulation of cells in the G2/M phase.
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Affiliation(s)
- Marcel Rak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Menge
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Roberta Tesch
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena M Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Dimitrios-Ilias Balourdas
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ekaterina Shevchenko
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Ismahan Abdi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Laurenz M Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, 70210 Kuopio, Finland
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Translational Cancer Network (DKTK) and Frankfurt Cancer Institute (FCI), 60438 Frankfurt am Main, Germany
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31
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Kuralt V, Frlan R. Navigating the Chemical Space of ENR Inhibitors: A Comprehensive Analysis. Antibiotics (Basel) 2024; 13:252. [PMID: 38534687 DOI: 10.3390/antibiotics13030252] [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: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance is a global health threat that requires innovative strategies against drug-resistant bacteria. Our study focuses on enoyl-acyl carrier protein reductases (ENRs), in particular FabI, FabK, FabV, and InhA, as potential antimicrobial agents. Despite their promising potential, the lack of clinical approvals for inhibitors such as triclosan and isoniazid underscores the challenges in achieving preclinical success. In our study, we curated and analyzed a dataset of 1412 small molecules recognized as ENR inhibitors, investigating different structural variants. Using advanced cheminformatic tools, we mapped the physicochemical landscape and identified specific structural features as key determinants of bioactivity. Furthermore, we investigated whether the compounds conform to Lipinski rules, PAINS, and Brenk filters, which are crucial for the advancement of compounds in development pipelines. Furthermore, we investigated structural diversity using four different representations: Chemotype diversity, molecular similarity, t-SNE visualization, molecular complexity, and cluster analysis. By using advanced bioinformatics tools such as matched molecular pairs (MMP) analysis, machine learning, and SHAP analysis, we were able to improve our understanding of the activity cliques and the precise effects of the functional groups. In summary, this chemoinformatic investigation has unraveled the FAB inhibitors and provided insights into rational antimicrobial design, seamlessly integrating computation into the discovery of new antimicrobial agents.
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Affiliation(s)
- Vid Kuralt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
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32
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Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG. Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening. RSC Chem Biol 2024; 5:209-215. [PMID: 38456036 PMCID: PMC10915964 DOI: 10.1039/d3cb00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
PHD fingers are a type of chromatin reader that primarily recognize chromatin as a function of lysine methylation state. Dysregulated PHD fingers are implicated in various human diseases, including acute myeloid leukemia. Targeting PHD fingers with small molecules is considered challenging as their histone tail binding pockets are often shallow and surface-exposed. The KDM5A PHD1 finger regulates the catalytic activity of KDM5A, an epigenetic enzyme often misregulated in cancers. To identify ligands that disrupt the PHD1-histone peptide interaction, we conducted a high-throughput screen and validated hits by orthogonal methods. We further elucidated structure-activity relationships in two classes of compounds to identify features important for binding. Our investigation offers a starting point for further optimization of small molecule PHD1 ligands.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Sophia L Qin
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Gregory M Lee
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Michelle R Arkin
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
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33
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Jairajpuri DS, Mohammad T, Hussain A, Amir S, Fatima U, AlAjmi MF, Yadav DK, Hassan MI. An integrated docking and molecular dynamics simulation approach to discover potential inhibitors of activin receptor-like kinase 1. J Mol Recognit 2024; 37:e3069. [PMID: 38053481 DOI: 10.1002/jmr.3069] [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: 09/08/2023] [Revised: 10/20/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023]
Abstract
Activin receptor-like kinase 1 (ALK1) is a transmembrane receptor involved in crucial signaling pathways associated with angiogenesis and vascular development. Inhibition of ALK1 signaling has emerged as a promising therapeutic strategy for various angiogenesis-related diseases, including cancer and hereditary hemorrhagic telangiectasia. This study aimed to investigate the potential of phytoconstituents as inhibitors of ALK1 using a combined approach of virtual screening and molecular dynamics (MDs) simulations. Phytoconstituents from the IMPPAT 2.0 database underwent virtual screening to identify potential inhibitors of ALK1. The compounds were initially filtered based on physicochemical parameters, following Lipinski's rules and the PAINS filter. Subsequently, compounds demonstrating high binding affinities in docking analysis were further analyzed. Additional assessments, including ADMET, PAINS, and PASS evaluations, were conducted to identify more potent hits. Through interaction analysis, a phytoconstituent, Candidine, exhibited appreciable affinity and specific interactions with the ALK1 active site. To validate the results, MD simulations and principal components analysis were performed. The MD simulations demonstrated that Candidine stabilized the ALK1 structure and reduced conformational fluctuations. In conclusion, Candidine shows promising potential as binding partners of ALK1. These findings provide a foundation for further exploration and development of Candidine as a lead molecule for therapeutic interventions targeting ALK1-associated diseases.
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Affiliation(s)
- Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Samira Amir
- Department of Chemistry, King Saud University, Riyadh, Saudi Arabia
| | - Urooj Fatima
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, Republic of Korea
- Arontier Co., Seoul, Republic of Korea
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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34
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Isigkeit L, Kärcher A, Adouvi G, Arifi S, Merk D. Rational design and virtual screening identify mimetics of the RXR agonist valerenic acid. ChemMedChem 2024; 19:e202300379. [PMID: 38235922 DOI: 10.1002/cmdc.202300379] [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: 07/22/2023] [Revised: 12/23/2023] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
The ligand-sensing transcription factor retinoid X receptor (RXR) is the universal heterodimer partner of nuclear receptors and involved in multiple physiological processes. Its pharmacological modulation holds therapeutic potential in cancer and neurodegeneration but many available RXR ligands lack specificity. The sesquiterpenoid valerenic acid has been identified as RXR agonist with unprecedented subtype and homodimer preference. Here, we identified simplified mimetics of the complex natural product by rational design and virtual screening that exhibited similar activity profiles on RXR and informed about structural elements contributing to the favorable activity.
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Affiliation(s)
- Laura Isigkeit
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Annette Kärcher
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Gustave Adouvi
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Silvia Arifi
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
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35
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Avellaneda-Tamayo JF, Chávez-Hernández AL, Prado-Romero DL, Medina-Franco JL. Chemical Multiverse and Diversity of Food Chemicals. J Chem Inf Model 2024; 64:1229-1244. [PMID: 38356237 PMCID: PMC10900296 DOI: 10.1021/acs.jcim.3c01617] [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: 10/05/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Food chemicals have a fundamental role in our lives, with an extended impact on nutrition, disease prevention, and marked economic implications in the food industry. The number of food chemical compounds in public databases has substantially increased in the past few years, which can be characterized using chemoinformatics approaches. We and other groups explored public food chemical libraries containing up to 26,500 compounds. This study aimed to analyze the chemical contents, diversity, and coverage in the chemical space of food chemicals and additives and, from here on, food components. The approach to food components addressed in this study is a public database with more than 70,000 compounds, including those predicted via omics techniques. It was concluded that food components have distinctive physicochemical properties and constitutional descriptors despite sharing many chemical structures with natural products. Food components, on average, have large molecular weights and several apolar structures with saturated hydrocarbons. Compared to reference databases, food component structures have low scaffold and fingerprint-based diversity and high structural complexity, as measured by the fraction of sp3 carbons. These structural features are associated with a large fraction of macronutrients as lipids. Lipids in food components were decompiled by an analysis of the maximum common substructures. The chemical multiverse representation of food chemicals showed a larger coverage of chemical space than natural products and FDA-approved drugs by using different sets of representations.
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Affiliation(s)
- Juan F. Avellaneda-Tamayo
- DIFACQUIM Research Group, Department
of Pharmacy, School of Chemistry, Universidad
Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Ana L. Chávez-Hernández
- DIFACQUIM Research Group, Department
of Pharmacy, School of Chemistry, Universidad
Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Diana L. Prado-Romero
- DIFACQUIM Research Group, Department
of Pharmacy, School of Chemistry, Universidad
Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department
of Pharmacy, School of Chemistry, Universidad
Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
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36
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Cui Y, Lanne A, Peng X, Browne E, Bhatt A, Coltman NJ, Craven P, Cox LR, Cundy NJ, Dale K, Feula A, Frampton J, Fung M, Morton M, Goff A, Salih M, Lang X, Li X, Moon C, Pascoe J, Portman V, Press C, Schulz-Utermoehl T, Lee S, Tortorella MD, Tu Z, Underwood ZE, Wang C, Yoshizawa A, Zhang T, Waddell SJ, Bacon J, Alderwick L, Fossey JS, Neagoie C. Azetidines Kill Multidrug-Resistant Mycobacterium tuberculosis without Detectable Resistance by Blocking Mycolate Assembly. J Med Chem 2024; 67:2529-2548. [PMID: 38331432 PMCID: PMC10895678 DOI: 10.1021/acs.jmedchem.3c01643] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024]
Abstract
Tuberculosis (TB) is the leading cause of global morbidity and mortality resulting from infectious disease, with over 10.6 million new cases and 1.4 million deaths in 2021. This global emergency is exacerbated by the emergence of multidrug-resistant MDR-TB and extensively drug-resistant XDR-TB; therefore, new drugs and new drug targets are urgently required. From a whole cell phenotypic screen, a series of azetidines derivatives termed BGAz, which elicit potent bactericidal activity with MIC99 values <10 μM against drug-sensitive Mycobacterium tuberculosis and MDR-TB, were identified. These compounds demonstrate no detectable drug resistance. The mode of action and target deconvolution studies suggest that these compounds inhibit mycobacterial growth by interfering with cell envelope biogenesis, specifically late-stage mycolic acid biosynthesis. Transcriptomic analysis demonstrates that the BGAz compounds tested display a mode of action distinct from the existing mycobacterial cell wall inhibitors. In addition, the compounds tested exhibit toxicological and PK/PD profiles that pave the way for their development as antitubercular chemotherapies.
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Affiliation(s)
- Yixin Cui
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alice Lanne
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Xudan Peng
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Edward Browne
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Apoorva Bhatt
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Nicholas J. Coltman
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Philip Craven
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Liam R. Cox
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Nicholas J. Cundy
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Katie Dale
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Antonio Feula
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Jon Frampton
- College of
Medical and Dental Sciences, University
of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Martin Fung
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Michael Morton
- ApconiX
Ltd, BIOHUB at Alderly Park, Nether Alderly, Cheshire SK10 4TG, U.K.
| | - Aaron Goff
- Department
of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PX, U.K.
| | - Mariwan Salih
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Xingfen Lang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Xingjian Li
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Chris Moon
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Jordan Pascoe
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Vanessa Portman
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Cara Press
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Timothy Schulz-Utermoehl
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Suki Lee
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Micky D. Tortorella
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Zhengchao Tu
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Zoe E. Underwood
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Changwei Wang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Akina Yoshizawa
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Tianyu Zhang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Simon J. Waddell
- Department
of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PX, U.K.
| | - Joanna Bacon
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Luke Alderwick
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
- Discovery
Sciences, Charles River Laboratories, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - John S. Fossey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Cleopatra Neagoie
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
- Visiting
Scientist, School of Chemistry, University
of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
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37
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Feoli A, Sarno G, Castellano S, Sbardella G. DMSO-Related Effects on Ligand-Binding Properties of Lysine Methyltransferases G9a and SETD8. Chembiochem 2024; 25:e202300809. [PMID: 38205880 DOI: 10.1002/cbic.202300809] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/12/2024]
Abstract
Being the standard solvent for preparing stock solutions of compounds for drug discovery, DMSO is always present in assay buffers in concentrations ranging from 0.1 % to 5 % (v/v). Even at the lowest concentrations, DMSO-containing solutions can have significant effects on individual proteins and possible pitfalls cannot be eliminated. Herein, we used two protein systems, the lysine methyltransferases G9a/KMT1 C and SETD8/KMT5 A, to study the effects of DMSO on protein stability and on the binding of the corresponding inhibitors, using different biophysical methods such as nano Differential Scanning Fluorimetry (nanoDSF), Differential Scanning Fluorimetry (DSF), microscale thermophoresis (MST), and surface plasmon resonance (SPR), all widely used in drug discovery screening campaigns. We demonstrated that the effects of DMSO are protein- and technique-dependent and cannot be predicted or extrapolated on the basis of previous studies using different proteins and/or different assays. Moreover, we showed that the application of orthogonal biophysical methods can lead to different binding affinity data, thus confirming the importance of using at least two different orthogonal assays in screening campaigns. This variability should be taken into account in the selection and characterization of hit compounds, in order to avoid data misinterpretation.
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Affiliation(s)
- Alessandra Feoli
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
| | - Giuliana Sarno
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
- PhD Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, I-84084, Fisciano, SA, Italy
| | - Sabrina Castellano
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
| | - Gianluca Sbardella
- Epigenetic Med Chem Lab, Department of Pharmacy, University of Salerno, via Giovanni Paolo II 132, 84084, Fisciano, SA, Italy
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38
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Khodair AI, El-Hallouty SM, Cagle-White B, Abdel Aziz MH, Hanafy MK, Mowafy S, Hamdy NM, Kassab SE. Camptothecin structure simplification elaborated new imidazo[2,1-b]quinazoline derivative as a human topoisomerase I inhibitor with efficacy against bone cancer cells and colon adenocarcinoma. Eur J Med Chem 2024; 265:116049. [PMID: 38185054 DOI: 10.1016/j.ejmech.2023.116049] [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: 10/03/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Camptothecin is a pentacyclic natural alkaloid that inhibits the hTop1 enzyme involved in DNA transcription and cancer cell growth. Camptothecin structure pitfalls prompted us to design new congeners using a structure simplification strategy to reduce the ring extension number from pentacyclic to tetracyclic while maintaining potential stacking of the new compounds with the DNA base pairs at the Top1-mediated cleavage complex and aqueous solubility, as well as minimizing compound-liver toxicity. The principal axis of this study was the verification of hTop1 inhibiting activity as a possible mechanism of action and the elaboration of new simplified inhibitors with improved pharmacodynamic and pharmacokinetic profiling using three structure panels (A-C) of (isoquinolinoimidazoquinazoline), (imidazoquinazoline), and (imidazoisoquinoline), respectively. DNA relaxation assay identified five compounds as hTop1 inhibitors belonging to the imidazoisoquinolines 3a,b, the imidazoquinazolines 12, and the isoquinolinoimidazoquinazolines 7a,b. In an MTT cytotoxicity assay against different cancer cell lines, compound 12 was the most potent against HOS bone cancer cells (IC50 = 1.47 μM). At the same time, the other inhibitors had no detectable activity against any cancer cell type. Compound (12) demonstrated great penetrating power in the HOS cancer cells' 3D-multicellular tumor spheroid model. Bioinformatics research of the hTop1 gene revealed that the TP53 cell proliferative gene is in the network of hTop1. The finding is confirmed empirically using the gene expression assay that proved the increase in p53 expression. The impact of structure simplification on compound 12 profile, characterized by the absence of acute oral liver toxicity when compared to Doxorubicin as a standard inhibitor, the lethal dose measured on Swiss Albino female mice and reported at LD50 = 250 mg/kg, and therapeutic significance in reducing colon adenocarcinoma tumor volume by 75.36 % after five weeks of treatment with compound 12. The molecular docking solutions of the active CPT-based derivative 12 and the inactive congener 14 into the active site of hTop1 and the activity cliffing of such MMP directed us to recommend the addition of HBD and HBA variables to compound 12 imidazoquinazoline core scaffold to enhance the potency via hydrogen bond formation with the major groove amino acids (Asp533, Lys532) as well as maintaining the hydrogen bond with the minor groove amino acid Arg364.
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Affiliation(s)
- Ahmed I Khodair
- Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516, Kafrelsheikh, Egypt.
| | - Salwa M El-Hallouty
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt
| | - Brittnee Cagle-White
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - May H Abdel Aziz
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - Mahmoud Kh Hanafy
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt; Research Centre for Idling Brain Science, Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Science, University of Toyama, 930-0194, Japan
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt
| | - Nadia M Hamdy
- Biochemistry Dept., Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt.
| | - Shaymaa E Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt.
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39
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Tandi M, Tripathi N, Gaur A, Gopal B, Sundriyal S. Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application. Mol Divers 2024; 28:37-50. [PMID: 36574164 DOI: 10.1007/s11030-022-10588-1] [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: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022]
Abstract
Virtual screening (VS) is an important approach in drug discovery and relies on the availability of a virtual library of synthetically tractable molecules. Ugi reaction (UR) represents an important multi-component reaction (MCR) that reliably produces a peptidomimetic scaffold. Recent literature shows that a tactically assembled Ugi adduct can be subjected to further chemical modifications to yield a variety of rings and scaffolds, thus, renewing the interest in this old reaction. Given the reliability and efficiency of UR, we collated an UR derived library (URDL) of small molecules (total = 5773) for VS. The synthesis of the majority of URDL molecules may be carried out in 1-2 pots in a time and cost-effective manner. The detailed analysis of the average property and chemical space of URDL was also carried out using the open-source Datawarrior program. The comparison with FDA-approved oral drugs and inhibitors of protein-protein interactions (iPPIs) suggests URDL molecules are 'clean', drug-like, and conform to a structurally distinct space from the other two categories. The average physicochemical properties of compounds in the URDL library lie closer to iPPI molecules than oral drugs thus suggesting that the URDL resource can be applied to discover novel iPPI molecules. The URDL molecules consist of diverse ring systems, many of which have not been exploited yet for drug design. Thus, URDL represents a small virtual library of drug-like molecules with unexplored chemical space designed for VS. The structures of all molecules of URDL, oral drugs, and iPPI compounds are being made freely accessible as supplementary information for broader application.
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Affiliation(s)
- Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Nancy Tripathi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Animesh Gaur
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | | | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.
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40
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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41
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Azzouzi M, Azougagh O, Ouchaoui AA, El hadad SE, Mazières S, Barkany SE, Abboud M, Oussaid A. Synthesis, Characterizations, and Quantum Chemical Investigations on Imidazo[1,2- a]pyrimidine-Schiff Base Derivative: ( E)-2-Phenyl- N-(thiophen-2-ylmethylene)imidazo[1,2- a]pyrimidin-3-amine. ACS OMEGA 2024; 9:837-857. [PMID: 38222514 PMCID: PMC10785637 DOI: 10.1021/acsomega.3c06841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 11/17/2023] [Indexed: 01/16/2024]
Abstract
In this study, (E)-2-phenyl-N-(thiophen-2-ylmethylene)imidazo[1,2-a]pyrimidin-3-amine (3) is synthesized, and detailed spectral characterizations using 1H NMR, 13C NMR, mass, and Fourier transform infrared (FT-IR) spectroscopy were performed. The optimized geometry was computed using the density functional theory method at the B3LYP/6-311++G(d,p) basis set. The theoretical FT-IR and NMR (1H and 13C) analysis are agreed to validate the structural assignment made for (3). Frontier molecular orbitals, molecular electrostatic potential, Mulliken atomic charge, electron localization function, localized orbital locator, natural bond orbital, nonlinear optical, Fukui functions, and quantum theory of atoms in molecules analyses are undertaken and meticulously interpreted, providing profound insights into the molecular nature and behaviors. In addition, ADMET and drug-likeness studies were carried out and investigated. Furthermore, molecular docking and molecular dynamics simulations have been studied, indicating that this is an ideal molecule to develop as a potential vascular endothelial growth factor receptor-2 inhibitor.
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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
| | - Omar Azougagh
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Abderrahim Ait Ouchaoui
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Salah eddine El hadad
- Laboratory
of Medical Biotechnology (MedBiotech), Bionova Research Center, Medical
and Pharmacy School, Mohammed V University, Agdal, Rabat B.P 8007, Morocco
| | - Stéphane Mazières
- Laboratory
of IMRCP, University Paul Sabatier, CNRS
UMR 5623, 118 route de Narbonne, Toulouse 31062, France
| | - Soufian El Barkany
- Laboratory
of Molecular Chemistry, Materials and Environment (LCM2E), Department
of Chemistry, Multidisciplinary Faculty of Nador, University Mohamed I, Nador 60700, Morocco
| | - Mohamed Abboud
- Catalysis
Research Group (CRG), Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - 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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42
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Xu Y, Wagner GK. A cell-permeable probe for the labelling of a bacterial glycosyltransferase and virulence factor. RSC Chem Biol 2024; 5:55-62. [PMID: 38179196 PMCID: PMC10763556 DOI: 10.1039/d3cb00092c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical probes for bacterial glycosyltransferases are of interest for applications such as tracking of expression levels, and strain profiling and identification. Existing probes for glycosyltransferases are typically based on sugar-nucleotides, whose charged nature limits their applicability in intact cells. We report the development of an uncharged covalent probe for the bacterial galactosyltransferase LgtC, and its application for the fluorescent labelling of this enzyme in recombinant form, cell lysates, and intact cells. The probe was designed by equipping a previously reported covalent LgtC inhibitor based on a pyrazol-3-one scaffold with a 7-hydroxycoumarin fluorophore. We show that this pyrazol-3-ones scaffold is surprisingly stable in aqueous media, which may have wider implications for the use of pyrazol-3-ones as chemical probes. We also show that the 7-hydroxycoumarin fluorophore leads to an unexpected improvement in activity, which could be exploited for the development of second generation analogues. These results will provide a basis for the development of LgtC-specific probes for the detection of LgtC-expressing bacterial strains.
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Affiliation(s)
- Yong Xu
- Department of Chemistry, King's College London UK
| | - Gerd K Wagner
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road Belfast BT9 7BL UK
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43
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Rostamighadi M, Kamelshahroudi A, Mehta V, Zeng FY, Pass I, Chung TDY, Salavati R. High-throughput screening of compounds targeting RNA editing in Trypanosoma brucei: Novel molecular scaffolds with broad trypanocidal effects. Biochem Pharmacol 2024; 219:115937. [PMID: 37995979 DOI: 10.1016/j.bcp.2023.115937] [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: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Mitochondrial uridine insertion/deletion RNA editing, catalyzed by a multiprotein complex (editosome), is essential for gene expression in trypanosomes and Leishmania parasites. As this process is absent in the human host, a drug targeting this mechanism promises high selectivity and reduced toxicity. Here, we successfully miniaturized our FRET-based full-round RNA editing assay, which replicates the complete RNA editing process, adapting it into a 1536-well format. Leveraging this assay, we screened over 100,000 compounds against purified editosomes derived from Trypanosoma brucei, identifying seven confirmed primary hits. We sourced and evaluated various analogs to enhance the inhibitory and parasiticidal effects of these primary hits. In combination with secondary assays, our compounds marked inhibition of essential catalytic activities, including the RNA editing ligase and interactions of editosome proteins. Although the primary hits did not exhibit any growth inhibitory effect on parasites, we describe eight analog compounds capable of effectively killing T. brucei and/or Leishmania donovani parasites within a low micromolar concentration. Whether parasite killing is - at least in part - due to inhibition of RNA editing in vivo remains to be assessed. Our findings introduce novel molecular scaffolds with the potential for broad antitrypanosomal effects.
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Affiliation(s)
- Mojtaba Rostamighadi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Arezou Kamelshahroudi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Vaibhav Mehta
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Fu-Yue Zeng
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Ian Pass
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Thomas D Y Chung
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
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44
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Olmedo DA, Durant-Archibold AA, López-Pérez JL, Medina-Franco JL. Design and Diversity Analysis of Chemical Libraries in Drug Discovery. Comb Chem High Throughput Screen 2024; 27:502-515. [PMID: 37409545 DOI: 10.2174/1386207326666230705150110] [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: 04/05/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
Chemical libraries and compound data sets are among the main inputs to start the drug discovery process at universities, research institutes, and the pharmaceutical industry. The approach used in the design of compound libraries, the chemical information they possess, and the representation of structures, play a fundamental role in the development of studies: chemoinformatics, food informatics, in silico pharmacokinetics, computational toxicology, bioinformatics, and molecular modeling to generate computational hits that will continue the optimization process of drug candidates. The prospects for growth in drug discovery and development processes in chemical, biotechnological, and pharmaceutical companies began a few years ago by integrating computational tools with artificial intelligence methodologies. It is anticipated that it will increase the number of drugs approved by regulatory agencies shortly.
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Affiliation(s)
- Dionisio A Olmedo
- Centro de Investigaciones Farmacognósticas de la Flora Panameña (CIFLORPAN), Facultad de Farmacia, Universidad de Panamá, Ciudad de Panamá, Apartado, 0824-00178, Panamá
- Sistema Nacional de Investigación (SNI), Secretaria Nacional de Ciencia, Tecnología e Innovación (SENACYT), Ciudad del Saber, Clayton, Panamá
| | - Armando A Durant-Archibold
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Apartado, 0843-01103, Panamá
- Departamento de Bioquímica, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panamá
| | - José Luis López-Pérez
- CESIFAR, Departamento de Farmacología, Facultad de Medicina, Universidad de Panamá, Ciudad de Panamá, Panamá
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Avda. Campo Charro s/n, 37071 Salamanca, España
| | - José Luis Medina-Franco
- DIFACQUIM Grupo de Investigación, Departamento de Farmacia, Escuela de Química, Universidad Nacional Autónoma de México, Ciudad de México, Apartado, 04510, México
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45
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Boateng ST, Roy T, Agbo ME, Mahmud MA, Banang-Mbeumi S, Chamcheu RCN, Yadav RK, Bramwell M, Pham LK, Dang DD, Jackson KE, Nagalo BM, Hill RA, Efimova T, Fotie J, Chamcheu JC. Multifaceted approach toward mapping out the anticancer properties of small molecules via in vitro evaluation on melanoma and nonmelanoma skin cancer cells, and in silico target fishing. Chem Biol Drug Des 2024; 103:e14418. [PMID: 38230791 DOI: 10.1111/cbdd.14418] [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: 05/14/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 01/18/2024]
Abstract
Melanoma and nonmelanoma skin cancers are among the most prevalent and most lethal forms of skin cancers. To identify new lead compounds with potential anticancer properties for further optimization, in vitro assays combined with in-silico target fishing and docking have been used to identify and further map out the antiproliferative and potential mode of action of molecules from a small library of compounds previously prepared in our laboratory. From screening these compounds in vitro against A375, SK-MEL-28, A431, and SCC-12 skin cancer cell lines, 35 displayed antiproliferative activities at the micromolar level, with the majority being primarily potent against the A431 and SCC-12 squamous carcinoma cell lines. The most active compounds 11 (A431: IC50 = 5.0 μM, SCC-12: IC50 = 2.9 μM, SKMEL-28: IC50 = 4.9 μM, A375: IC50 = 6.7 μM) and 13 (A431: IC50 = 5.0 μM, SCC-12: IC50 = 3.3 μM, SKMEL-28: IC50 = 13.8 μM, A375: IC50 = 17.1 μM), significantly and dose-dependently induced apoptosis of SCC-12 and SK-MEL-28 cells, as evidenced by the suppression of Bcl-2 and upregulation of Bax, cleaved caspase-3, caspase-9, and PARP protein expression levels. Both agents significantly reduced scratch wound healing, colony formation, and expression levels of deregulated cancer molecular targets including RSK/Akt/ERK1/2 and S6K1. In silico target prediction and docking studies using the SwissTargetPrediction web-based tool suggested that CDK8, CLK4, nuclear receptor ROR, tyrosine protein-kinase Fyn/LCK, ROCK1/2, and PARP, all of which are dysregulated in skin cancers, might be prospective targets for the two most active compounds. Further validation of these targets by western blot analyses, revealed that ROCK/Fyn and its associated Hedgehog (Hh) pathways were downregulated or modulated by the two lead compounds. In aggregate, these results provide a strong framework for further validation of the observed activities and the development of a more comprehensive structure-activity relationship through the preparation and biological evaluation of analogs.
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Affiliation(s)
- Samuel T Boateng
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Tithi Roy
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Mercy E Agbo
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Md Ashiq Mahmud
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Sergette Banang-Mbeumi
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Roxane-Cherille N Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Rajesh K Yadav
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Marion Bramwell
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Long K Pham
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Danny D Dang
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Keith E Jackson
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Bolni Marius Nagalo
- Department of Pathology, University of Arkansas for Medical Sciences (UAMS), Little Rock, Arkansas, USA
- The Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Science (UAMS), Little Rock, Arkansas, USA
| | - Ronald A Hill
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
| | - Tatiana Efimova
- Department of Biomedical Engineering, Northwestern University, Chicago, Illinois, USA
| | - Jean Fotie
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana, USA
| | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana - Monroe, Monroe, Louisiana, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
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46
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Hernandez RD, Genio FAF, Casanova JR, Conato MT, Paderes MC. Antiproliferative Activities and SwissADME Predictions of Physicochemical Properties of Carbonyl Group-Modified Rotenone Analogues. ChemistryOpen 2024; 13:e202300087. [PMID: 37590423 PMCID: PMC10784630 DOI: 10.1002/open.202300087] [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: 05/24/2023] [Revised: 07/18/2023] [Indexed: 08/19/2023] Open
Abstract
Rotenone is a naturally occurring compound shown to exhibit antiproliferative activity against various cancer cell lines, indicating its potential as a lead anticancer agent. However, its toxicity against normal cells has prompted further investigation and chemical modifications. In this study, a library of carbonyl group-modified rotenone derivatives was synthesized and evaluated for their antiproliferative activities against MCF-7 breast cancer cells, A549 human lung carcinoma cells, and HCT116 human colorectal cancer cells using 3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide (MTT) assay. The results showed several promising compounds that inhibited cell proliferation. Specifically, the oxime and alcohol rotenone derivatives exhibited antiproliferative activities against all 3 cancer cell lines, while the ethoxy, carbamate, and alkene derivatives are selective against MCF-7 (IC50 =5.72 μM), HCT116 (IC50 =8.86 μM), and A549 (IC50 =0.11 μM), respectively. SwissADME analysis showed that the physicochemical properties and drug-likeness of the synthesized rotenone derivatives were within the set limits, suggesting the favorable characteristics of these compounds for drug development. The findings obtained in this work highlight the potential of rotenone derivatives as promising chemotherapeutic candidates.
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Affiliation(s)
- Rajelle D. Hernandez
- Institute of ChemistryUniversity of the Philippines DilimanQuezon CityPhilippines1101
| | | | - Jannelle R. Casanova
- Institute of ChemistryUniversity of the Philippines DilimanQuezon CityPhilippines1101
| | - Marlon T. Conato
- Institute of ChemistryUniversity of the Philippines DilimanQuezon CityPhilippines1101
| | - Monissa C. Paderes
- Institute of ChemistryUniversity of the Philippines DilimanQuezon CityPhilippines1101
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47
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Adouvi G, Nawa F, Ballarotto M, Rüger LA, Knümann L, Kasch T, Arifi S, Schubert-Zsilavecz M, Willems S, Marschner JA, Pabel J, Merk D. Structural Fusion of Natural and Synthetic Ligand Features Boosts RXR Agonist Potency. J Med Chem 2023; 66:16762-16771. [PMID: 38064686 DOI: 10.1021/acs.jmedchem.3c01435] [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: 12/29/2023]
Abstract
The retinoid X receptors (RXRs) are ligand-activated transcription factors involved in, for example, differentiation and apoptosis regulation. Currently used reference RXR agonists suffer from insufficient specificity and poor physicochemical properties, and improved tools are needed to capture the unexplored therapeutic potential of RXR. Endogenous vitamin A-derived RXR ligands and the natural product RXR agonist valerenic acid comprise acrylic acid residues with varying substitution patterns to engage the critical ionic contact with the binding site arginine. To mimic and exploit this natural ligand motif, we probed its structural fusion with synthetic RXR modulator scaffolds, which had profound effects on agonist activity and remarkably boosted potency of an oxaprozin-derived RXR agonist chemotype. Bioisosteric replacement of the acrylic acid to overcome its pan-assay interference compounds (PAINS) character enabled the development of a highly optimized RXR agonist chemical probe.
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Affiliation(s)
- Gustave Adouvi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Felix Nawa
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Marco Ballarotto
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Lorena Andrea Rüger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Loris Knümann
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Till Kasch
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Silvia Arifi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | | | - Sabine Willems
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian A Marschner
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jörg Pabel
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
- Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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48
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Byrne AJ, Bright SA, McKeown JP, Bergin A, Twamley B, McElligott AM, Noorani S, Kandwal S, Fayne D, O’Boyle NM, Williams DC, Meegan MJ. Synthesis and Pro-Apoptotic Effects of Nitrovinylanthracenes and Related Compounds in Chronic Lymphocytic Leukaemia (CLL) and Burkitt's Lymphoma (BL). Molecules 2023; 28:8095. [PMID: 38138584 PMCID: PMC10746112 DOI: 10.3390/molecules28248095] [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: 10/25/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a malignancy of the immune B lymphocyte cells and is the most common leukaemia diagnosed in developed countries. In this paper, we report the synthesis and antiproliferative effects of a series of (E)-9-(2-nitrovinyl)anthracenes and related nitrostyrene compounds in CLL cell lines and also in Burkitt's lymphoma (BL) cell lines, a rare form of non-Hodgkin's immune B-cell lymphoma. The nitrostyrene scaffold was identified as a lead structure for the development of effective compounds targeting BL and CLL. The series of structurally diverse nitrostyrenes was synthesised via Henry-Knoevenagel condensation reactions. Single-crystal X-ray analysis confirmed the structure of (E)-9-chloro-10-(2-nitrobut-1-en-1-yl)anthracene (19f) and the related 4-(anthracen-9-yl)-1H-1,2,3-triazole (30a). The (E)-9-(2-nitrovinyl)anthracenes 19a, 19g and 19i-19m were found to elicit potent antiproliferative effects in both BL cell lines EBV-MUTU-1 (chemosensitive) and EBV+ DG-75 (chemoresistant) with >90% inhibition at 10 μM. Selected (E)-9-(2-nitrovinyl)anthracenes demonstrated potent antiproliferative activity in CLL cell lines, with IC50 values of 0.17 μM (HG-3) and 1.3 μM (PGA-1) for compound 19g. The pro-apoptotic effects of the most potent compounds 19a, 19g, 19i, 19l and 19m were demonstrated in both CLL cell lines HG-3 and PGA-1. The (E)-nitrostyrene and (E)-9-(2-nitrovinyl)anthracene series of compounds offer potential for further development as novel chemotherapeutics for CLL.
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Affiliation(s)
- Andrew J. Byrne
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
| | - Sandra A. Bright
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (S.K.); (D.F.); (D.C.W.)
| | - James. P. McKeown
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
| | - Adam Bergin
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
| | - Brendan Twamley
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland;
| | - Anthony M. McElligott
- Discipline of Haematology, School of Medicine, Trinity Translational Medicine Institute, St. James’s Hospital and Trinity College, Dublin 8, D08 W9RT Dublin, Ireland;
| | - Sara Noorani
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
| | - Shubhangi Kandwal
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (S.K.); (D.F.); (D.C.W.)
| | - Darren Fayne
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (S.K.); (D.F.); (D.C.W.)
| | - Niamh M. O’Boyle
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
| | - D. Clive Williams
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (S.K.); (D.F.); (D.C.W.)
| | - Mary J. Meegan
- School of Pharmacy and Pharmaceutical Sciences, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, D02 R590 Dublin, Ireland (J.P.M.); (M.J.M.)
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49
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Pham L, Jiang R, Liu Z, Nguyen M, Nguyen Y, Gong Y, Bi Y, Kim HR, Kim YR, Kim G. Synthesis of 9-Cinnamyl-9 H-purine Derivatives as Novel TLR4/MyD88/NF-κB Pathway Inhibitors for Anti-inflammatory Effects. ACS Med Chem Lett 2023; 14:1839-1847. [PMID: 38116448 PMCID: PMC10726439 DOI: 10.1021/acsmedchemlett.3c00437] [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: 09/27/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
The novel 9-cinnamyl-9H-purine skeleton, inspired by resveratrol and curcumin, was developed to avoid a pan-assay interference compound (PAINS) related to invalid metabolic pancreas activity (IMPS). It replaced the phenol group with purine analogues, the building blocks of DNA and RNA. Alterations to the hydroxyl group in the cinnamyl group, such as H, Me, or F substitutions, were made to impede its oxidation to a PAINS-associated quinone. Among the compounds tested, 5e significantly inhibited nitric oxide production in LPS-induced macrophages (IC50: 6.4 vs 26.4 μM for resveratrol). 5e also reduced pro-inflammatory cytokine levels (IL-6, TNF-α, IL-1β) and lowered iNOS and COX-2 protein levels. Mechanistically, 5e disrupted the TLR4-MyD88 protein interaction, leading to the suppression of the NF-κB signaling pathway suppression. In an atopic dermatitis mouse model, 5e reduced ear edema and inflammation. These findings indicate that the novel 9-cinnamyl-9H-purine skeleton provides therapeutic insight into treating various human diseases by regulating inflammation.
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Affiliation(s)
- Linh Pham
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Rui Jiang
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Zijing Liu
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Mai Nguyen
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yen Nguyen
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yue Gong
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Yanran Bi
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Hong-Rae Kim
- Department
of Biomedical Sciences, College of Medicine, Korea University, Seoul 02708, Korea
| | - Young Ran Kim
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
| | - Gyudong Kim
- College
of Pharmacy and Research Institute of Drug Development, Chonnam National University, Gwangju 61186, Korea
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50
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Ouassaf M, Bourougaa L, Al-Mijalli SH, Abdallah EM, Bhat AR, A. Kawsar SM. Marine-Derived Compounds as Potential Inhibitors of Hsp90 for Anticancer and Antimicrobial Drug Development: A Comprehensive In Silico Study. Molecules 2023; 28:8074. [PMID: 38138564 PMCID: PMC10871121 DOI: 10.3390/molecules28248074] [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: 11/05/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Marine compounds constitute a diverse and invaluable resource for the discovery of bioactive substances with promising applications in the pharmaceutical development of anti-inflammatory and antibacterial agents. In this study, a comprehensive methodology was employed, encompassing pharmacophore modeling, virtual screening, in silico ADMET assessment (encompassing aspects of absorption, distribution, metabolism, excretion, and toxicity), and molecular dynamics simulations. These methods were applied to identify new inhibitors targeting the Hsp90 protein (heat shock protein 90), commencing with a diverse assembly of compounds sourced from marine origins. During the virtual screening phase, an extensive exploration was conducted on a dataset comprising 31,488 compounds sourced from the CMNPD database, characterized by a wide array of molecular structures. The principal objective was the development of structure-based pharmacophore models, a valuable approach when the pool of known ligands is limited. The pharmacophore model DDRRR was successfully constructed within the active sites of the Hsp90 crystal structure. Subsequent docking studies led to the identification of six compounds (CMNPD 22591, 9335, 10015, 360799, 15115, and 20988) demonstrating substantial binding affinities, each with values below -8.3 kcal/mol. In the realm of in silico ADMET predictions, five of these compounds exhibited favorable pharmacokinetic properties. Furthermore, molecular dynamics simulations and total binding energy calculations using MM-PBSA indicated that these marine-derived compounds formed exceptionally stable complexes with the Hsp90 receptor over a 100-nanosecond simulation period. These findings underscore the considerable potential of these novel marine compounds as promising candidates for anticancer and antimicrobial drug development.
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Affiliation(s)
- Mebarka Ouassaf
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Lotfi Bourougaa
- Group of Computational and Medicinal Chemistry, LMCE Laboratory, University of Biskra, Biskra 707000, Algeria;
| | - Samiah Hamad Al-Mijalli
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia;
| | - Ajmal R. Bhat
- Department of Chemistry, RTM Nagpur University, Nagpur 440033, India;
| | - Sarkar M. A. Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, Faculty of Science, University of Chittagong, Chittagong 4331, Bangladesh;
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