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Adessi TG, Wagner PM, Bisogno FR, Nicotra VE, Guido ME, García ME. Enhancing structural diversity through chemical engineering of Ambrosia tenuifolia extract for novel anti-glioblastoma compounds. Sci Rep 2024; 14:14229. [PMID: 38902325 PMCID: PMC11190268 DOI: 10.1038/s41598-024-63639-y] [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: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/22/2024] Open
Abstract
Natural products are an unsurpassed source of leading structures in drug discovery. The biosynthetic machinery of the producing organism offers an important source for modifying complex natural products, leading to analogs that are unattainable by chemical semisynthesis or total synthesis. In this report, through the combination of natural products chemistry and diversity-oriented synthesis, a diversity-enhanced extracts approach is proposed using chemical reactions that remodel molecular scaffolds directly on extracts of natural resources. This method was applied to subextract enriched in sesquiterpene lactones from Ambrosia tenuifolia (Fam. Asteraceae) using acid media conditions (p-toluenesulfonic acid) to change molecular skeletons. The chemically modified extract was then fractionated by a bioguided approach to obtain the pure compounds responsible for the anti-glioblastoma (GBM) activity in T98G cell cultures. Indeed, with the best candidate, chronobiological experiments were performed to evaluate temporal susceptibility to the treatment on GBM cell cultures to define the best time to apply the therapy. Finally, bioinformatics tools were used to supply qualitative and quantitative information on the physicochemical properties, chemical space, and structural similarity of the compound library obtained. As a result, natural products derivatives containing new molecular skeletons were obtained, with possible applications as chemotherapeutic agents against human GBM T98G cell cultures.
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Affiliation(s)
- Tonino G Adessi
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Paula M Wagner
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Fabricio R Bisogno
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC-CONICET), Córdoba, Argentina
| | - Viviana E Nicotra
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Mario E Guido
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET), Córdoba, Argentina
| | - Manuela E García
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC), Edificio de Ciencias Químicas 2, Haya de la Torre y Medina Allende, Ciudad Universitaria, CP X5000HUA, Córdoba, Argentina.
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.
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2
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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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3
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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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4
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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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5
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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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6
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Chen YK, Gahtani RM, Al Shahrani M, Hani U, Alshabrmi FM, Alam S, Almohaimeed HM, Basabrain AA, Shahab M, Xie MZ. Identification of potential inhibitors targeting Ebola virus VP35 protein: a computational strategy. J Biomol Struct Dyn 2023:1-13. [PMID: 38124513 DOI: 10.1080/07391102.2023.2294384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Ebola virus (EBOV) poses a severe threat as a highly infectious pathogen, causing devastating hemorrhagic fever in both humans and animals. The EBOV virus VP35 protein plays a crucial role in viral replication and exhibits the ability to suppress the host interferon cascade, leading to immune system depletion. As a potential drug target, VP35 protein inhibition holds promise for combating EBOV. To discover new drug candidates, we employed a computer-aided drug design approach, focusing on compounds capable of inhibiting VP35 protein replication. In this connection, a pharmacophore model was generated using molecular interactions between the VP35 protein and its inhibitor. ZINC and Cambridge database were screened using validated pharmacophore model. Further the compounds were filtered based on Lipinski's rule of five and subjected to MD simulation and relative binding free energy calculation. Six compounds manifest a significant docking score and strong binding interaction towards VP35 protein. MD simulations further confirmed the remarkable stability of these six complexes. Relative binding free energy calculations also showed significant ΔG value in the range of -132.3 and -49.3 kcal/mol. This study paves the way for further optimization of these compounds as potential inhibitors of VP35, facilitating subsequent experimental in vitro studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yan-Kun Chen
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
- Precision Medicine R&D Center, Zhuhai Institute of Advanced Technology, Zhuhai, China
| | - Reem M Gahtani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mesfer Al Shahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha,Saudia Arabia
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Sarfaraz Alam
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Hailah M Almohaimeed
- Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ammar A Basabrain
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Meng-Zhou Xie
- School of Chinese Medicine, Hunan University of Chinese Medicine, Changsha, China
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7
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Maresca L, Crivaro E, Migliorini F, Anichini G, Giammona A, Pepe S, Poggialini F, Vagaggini C, Giannini G, Sestini S, Borgognoni L, Lapucci A, Dreassi E, Taddei M, Manetti F, Petricci E, Stecca B. Targeting GLI1 and GLI2 with small molecule inhibitors to suppress GLI-dependent transcription and tumor growth. Pharmacol Res 2023; 195:106858. [PMID: 37473878 DOI: 10.1016/j.phrs.2023.106858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Aberrant activation of Hedgehog (HH) signaling in cancer is the result of genetic alterations of upstream pathway components (canonical) or other oncogenic mechanisms (noncanonical), that ultimately concur to activate the zinc-finger transcription factors GLI1 and GLI2. Therefore, inhibition of GLI activity is a good therapeutic option to suppress both canonical and noncanonical activation of the HH pathway. However, only a few GLI inhibitors are available, and none of them have the profile required for clinical development due to poor metabolic stability and aqueous solubility, and high hydrophobicity. Two promising quinoline inhibitors of GLI were selected by virtual screening and subjected to hit-to-lead optimization, thus leading to the identification of the 4-methoxy-8-hydroxyquinoline derivative JC19. This molecule impaired GLI1 and GLI2 activities in several cellular models interfering with the binding of GLI1 and GLI2 to DNA. JC19 suppressed cancer cell proliferation by enhancing apoptosis, inducing a strong anti-tumor response in several cancer cell lines in vitro. Specificity towards GLI1 and GLI2 was demonstrated by lower activity of JC19 in GLI1- or GLI2-depleted cancer cells. JC19 showed excellent metabolic stability and high passive permeability. Notably, JC19 inhibited GLI1-dependent melanoma xenograft growth in vivo, with no evidence of toxic effects in mice. These results highlight the potential of JC19 as a novel anti-cancer agent targeting GLI1 and GLI2.
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Affiliation(s)
- Luisa Maresca
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy
| | - Enrica Crivaro
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy; Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Francesca Migliorini
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Giulia Anichini
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy
| | - Alessandro Giammona
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy
| | - Sara Pepe
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy
| | - Federica Poggialini
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Chiara Vagaggini
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Serena Sestini
- Plastic and Reconstructive Surgery Unit Regional Melanoma Referral Center and Melanoma & Skin Cancer Unit, Santa Maria Annunziata Hospital, Florence, Italy
| | - Lorenzo Borgognoni
- Plastic and Reconstructive Surgery Unit Regional Melanoma Referral Center and Melanoma & Skin Cancer Unit, Santa Maria Annunziata Hospital, Florence, Italy
| | - Andrea Lapucci
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Elena Dreassi
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Maurizio Taddei
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Fabrizio Manetti
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
| | - Elena Petricci
- Dept. of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
| | - Barbara Stecca
- Core Research Laboratory - Institute for Cancer Research and Prevention (ISPRO), Florence, Italy.
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8
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De Lorenzi E, Seghetti F, Tarozzi A, Pruccoli L, Contardi C, Serra M, Bisi A, Gobbi S, Vistoli G, Gervasoni S, Argentini C, Ghirardo G, Guarato G, Orso G, Belluti F, Di Martino RMC, Zusso M. Targeting the multifaceted neurotoxicity of Alzheimer's disease by tailored functionalisation of the curcumin scaffold. Eur J Med Chem 2023; 252:115297. [PMID: 36996713 DOI: 10.1016/j.ejmech.2023.115297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Simultaneous modulation of multifaceted toxicity arising from neuroinflammation, oxidative stress, and mitochondrial dysfunction represents a valuable therapeutic strategy to tackle Alzheimer's disease. Among the significant hallmarks of the disorder, Aβ protein and its aggregation products are well-recognised triggers of the neurotoxic cascade. In this study, by tailored modification of the curcumin-based lead compound 1, we aimed at developing a small library of hybrid compounds targeting Aβ protein oligomerisation and the consequent neurotoxic events. Interestingly, from in vitro studies, analogues 3 and 4, bearing a substituted triazole moiety, emerged as multifunctional agents able to counteract Aβ aggregation, neuroinflammation and oxidative stress. In vivo proof-of-concept evaluations, performed in a Drosophila oxidative stress model, allowed us to identify compound 4 as a promising lead candidate.
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9
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Amado PM, Woodley C, Cristiano MLS, O’Neill PM. Recent Advances of DprE1 Inhibitors against Mycobacterium tuberculosis: Computational Analysis of Physicochemical and ADMET Properties. ACS OMEGA 2022; 7:40659-40681. [PMID: 36406587 PMCID: PMC9670723 DOI: 10.1021/acsomega.2c05307] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/21/2022] [Indexed: 05/14/2023]
Abstract
Decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1) is a critical flavoenzyme in Mycobacterium tuberculosis, catalyzing a vital step in the production of lipoarabinomannan and arabinogalactan, both of which are essential for cell wall biosynthesis. Due to its periplasmic localization, DprE1 is a susceptible target, and several compounds with diverse scaffolds have been discovered that inhibit this enzyme, covalently or noncovalently. We evaluated a total of ∼1519 DprE1 inhibitors disclosed in the literature from 2009 to April 2022 by performing an in-depth analysis of physicochemical descriptors and absorption, distribution, metabolism, excretion, and toxicity (ADMET), to gain new insights into these properties in DprE1 inhibitors. Several molecular properties that should facilitate the design and optimization of future DprE1 inhibitors are described, allowing for the development of improved analogues targeting M. tuberculosis.
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Affiliation(s)
- Patrícia
S. M. Amado
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Christopher Woodley
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Maria L. S. Cristiano
- Center
of Marine Sciences - CCMAR, University of
Algarve, P-8005-039 Faro, Portugal
- Department
of Chemistry and Pharmacy, FCT, University
of Algarve, P-8005-039 Faro, Portugal
- Email
for M.L.S.C.:
| | - Paul M. O’Neill
- Department
of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
- Email for P.M.O.:
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10
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Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors. Int J Mol Sci 2022; 23:ijms232213946. [PMID: 36430425 PMCID: PMC9694616 DOI: 10.3390/ijms232213946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Antifolates such as methotrexate (MTX) have been largely known as anticancer agents because of their role in blocking nucleic acid synthesis and cell proliferation. Their mechanism of action lies in their ability to inhibit enzymes involved in the folic acid cycle, especially human dihydrofolate reductase (hDHFR). However, most of them have a classical structure that has proven ineffective against melanoma, and, therefore, inhibitors with a non-classical lipophilic structure are increasingly becoming an attractive alternative to circumvent this clinical resistance. In this study, we conducted a protocol combining virtual screening (VS) and cell-based assays to identify new potential non-classical hDHFR inhibitors. Among 173 hit compounds identified (average logP = 3.68; average MW = 378.34 Da), two-herein, called C1 and C2-exhibited activity against melanoma cell lines B16 and A375 by MTT and Trypan-Blue assays. C1 showed cell growth arrest (39% and 56%) and C2 showed potent cytotoxic activity (77% and 51%) in a dose-dependent manner. The effects of C2 on A375 cell viability were greater than MTX (98% vs 60%) at equivalent concentrations and times. Our results indicate that the integrated in silico/in vitro approach provided a benchmark to identify novel promising non-classical DHFR inhibitors showing activity against melanoma cells.
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11
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Sheridan R, Spelman K. Polyphenolic promiscuity, inflammation-coupled selectivity: Whether PAINs filters mask an antiviral asset. Front Pharmacol 2022; 13:909945. [PMID: 36339544 PMCID: PMC9634583 DOI: 10.3389/fphar.2022.909945] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/03/2022] [Indexed: 11/26/2023] Open
Abstract
The Covid-19 pandemic has elicited much laboratory and clinical research attention on vaccines, mAbs, and certain small-molecule antivirals against SARS-CoV-2 infection. By contrast, there has been comparatively little attention on plant-derived compounds, especially those that are understood to be safely ingested at common doses and are frequently consumed in the diet in herbs, spices, fruits and vegetables. Examining plant secondary metabolites, we review recent elucidations into the pharmacological activity of flavonoids and other polyphenolic compounds and also survey their putative frequent-hitter behavior. Polyphenols, like many drugs, are glucuronidated post-ingestion. In an inflammatory milieu such as infection, a reversion back to the active aglycone by the release of β-glucuronidase from neutrophils and macrophages allows cellular entry of the aglycone. In the context of viral infection, virions and intracellular virus particles may be exposed to promiscuous binding by the polyphenol aglycones resulting in viral inhibition. As the mechanism's scope would apply to the diverse range of virus species that elicit inflammation in infected hosts, we highlight pre-clinical studies of polyphenol aglycones, such as luteolin, isoginkgetin, quercetin, quercetagetin, baicalein, curcumin, fisetin and hesperetin that reduce virion replication spanning multiple distinct virus genera. It is hoped that greater awareness of the potential spatial selectivity of polyphenolic activation to sites of pathogenic infection will spur renewed research and clinical attention for natural products antiviral assaying and trialing over a wide array of infectious viral diseases.
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Affiliation(s)
| | - Kevin Spelman
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, United States
- Health Education and Research, Driggs, ID, United States
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12
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Do XH, Hoang MHT, Vu AT, Nguyen LT, Bui DTT, Dinh DT, Nguyen XH, Than UTT, Mai HT, To TT, Nguyen TNH, Hoang NTM. Differential Cytotoxicity of Curcumin-Loaded Micelles on Human Tumor and Stromal Cells. Int J Mol Sci 2022; 23:ijms232012362. [PMID: 36293215 PMCID: PMC9604151 DOI: 10.3390/ijms232012362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022] Open
Abstract
Although curcumin in the form of nanoparticles has been demonstrated as a potential anti-tumor compound, the impact of curcumin and nanocurcumin in vitro on normal cells and in vivo in animal models is largely unknown. This study evaluated the toxicity of curcumin-loaded micelles in vitro and in vivo on several tumor cell lines, primary stromal cells, and zebrafish embryos. Breast tumor cell line (MCF7) and stromal cells (human umbilical cord vein endothelial cells, human fibroblasts, and human umbilical cord-derived mesenchymal stem cells) were used in this study. A zebrafish embryotoxicity (FET) assay was conducted following the Organisation for Economic Co-operation and Development (OECD) Test 236. Compared to free curcumin, curcumin PM showed higher cytotoxicity to MCF7 cells in both monolayer culture and multicellular tumor spheroids. The curcumin-loaded micelles efficiently penetrated the MCF7 spheroids and induced apoptosis. The nanocurcumin reduced the viability and disturbed the function of stromal cells by suppressing cell migration and tube formation. The micelles demonstrated toxicity to the development of zebrafish embryos. Curcumin-loaded micelles demonstrated toxicity to both tumor and normal primary stromal cells and zebrafish embryos, indicating that the use of nanocurcumin in cancer treatment should be carefully investigated and controlled.
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Affiliation(s)
- Xuan-Hai Do
- Department of Practical and Experimental Surgery, Vietnam Military Medical University, 160 Phung Hung Street, Phuc La, Ha Dong, Hanoi 10000, Vietnam
| | - My Hanh Thi Hoang
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
| | - Anh-Tuan Vu
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
| | - Lai-Thanh Nguyen
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
| | - Dung Thi Thuy Bui
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
| | - Duy-Thanh Dinh
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
- Laboratory for Organogenesis and Regeneration, GIGA-R, University of Liège, 4000 Liège, Belgium
| | - Xuan-Hung Nguyen
- Center of Applied Sciences, Regenerative Medicine and Advance Technologies (CARA), Vinmec Healthcare System, 458 Minh Khai Street, Hanoi 10000, Vietnam
- College of Health Sciences, Vin University, Hanoi 10000, Vietnam
| | - Uyen Thi Trang Than
- Center of Applied Sciences, Regenerative Medicine and Advance Technologies (CARA), Vinmec Healthcare System, 458 Minh Khai Street, Hanoi 10000, Vietnam
| | - Hien Thi Mai
- Center of Applied Sciences, Regenerative Medicine and Advance Technologies (CARA), Vinmec Healthcare System, 458 Minh Khai Street, Hanoi 10000, Vietnam
| | - Thuy Thanh To
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
| | - Tra Ngoc Huong Nguyen
- Department of Biology, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA
| | - Nhung Thi My Hoang
- Faculty of Biology, VNU University of Science, 334 Nguyen Trai Street, Hanoi 10000, Vietnam or
- Correspondence: ; Tel.: +84-947440249
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13
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Systematic Down-Selection of Repurposed Drug Candidates for COVID-19. Int J Mol Sci 2022; 23:ijms231911851. [PMID: 36233149 PMCID: PMC9569752 DOI: 10.3390/ijms231911851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 01/09/2023] Open
Abstract
SARS-CoV-2 is the cause of the COVID-19 pandemic which has claimed more than 6.5 million lives worldwide, devastating the economy and overwhelming healthcare systems globally. The development of new drug molecules and vaccines has played a critical role in managing the pandemic; however, new variants of concern still pose a significant threat as the current vaccines cannot prevent all infections. This situation calls for the collaboration of biomedical scientists and healthcare workers across the world. Repurposing approved drugs is an effective way of fast-tracking new treatments for recently emerged diseases. To this end, we have assembled and curated a database consisting of 7817 compounds from the Compounds Australia Open Drug collection. We developed a set of eight filters based on indicators of efficacy and safety that were applied sequentially to down-select drugs that showed promise for drug repurposing efforts against SARS-CoV-2. Considerable effort was made to evaluate approximately 14,000 assay data points for SARS-CoV-2 FDA/TGA-approved drugs and provide an average activity score for 3539 compounds. The filtering process identified 12 FDA-approved molecules with established safety profiles that have plausible mechanisms for treating COVID-19 disease. The methodology developed in our study provides a template for prioritising drug candidates that can be repurposed for the safe, efficacious, and cost-effective treatment of COVID-19, long COVID, or any other future disease. We present our database in an easy-to-use interactive interface (CoviRx that was also developed to enable the scientific community to access to the data of over 7000 potential drugs and to implement alternative prioritisation and down-selection strategies.
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14
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Swetha R, Sharma A, Singh R, Ganeshpurkar A, Kumar D, Kumar A, Singh SK. Combined ligand-based and structure-based design of PDE 9A inhibitors against Alzheimer's disease. Mol Divers 2022; 26:2877-2892. [PMID: 35932437 DOI: 10.1007/s11030-022-10504-7] [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: 06/02/2022] [Accepted: 07/22/2022] [Indexed: 10/16/2022]
Abstract
PDE9 enzyme hydrolyzes cGMP, which is involved in the regulation of synaptic plasticity through the NMDA pathway (a well-known excitotoxic target for AD) via activation of calcium/calmodulin-dependent neuronal NO synthases in the postsynaptic neurons. The inhibition of PDE9 leads to elevated cGMP levels, causing enhanced NMDA signaling and thus contributing to an increase in synaptic plasticity and stabilization. Therefore, it could be considered a pertinent target for AD drug discovery. PF-04447943 and BI-409306 targeting PDE9 are undergoing clinical trials (Phase II). The present study encompasses a pharmacophoric approach to identify potent PDE9 inhibitors using various computational methods. Pharmacophores generated from the PDB 6A3N yielded 37,554 virtual hits, which underwent drug likeliness and PAINS filtering to arrive at a few virtual leads. The leads were further subjected to extra precision docking, ADMET predictions, and molecular dynamics. The final hits, ZINC000001305675 and ZINC000000377099, showed superior docking scores of - 10.90 and - 10.30 kcal/mol and satisfactory predicted ADMET scores. The hits were subjected to molecular dynamics (MD) studies, wherein they formed stable complexes with PDE9 protein and had ligand RMSDs within acceptable limits. The processes involved in the combined ligand and structure-based strategies.
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Affiliation(s)
- Rayala Swetha
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Anjali Sharma
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ankit Ganeshpurkar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharti Vidyapeeth University, Pune, India
| | | | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil K Singh
- Pharmaceutical Chemistry Research Laboratory 1, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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15
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Targeting the HER3 pseudokinase domain with small molecule inhibitors. Methods Enzymol 2022; 667:455-505. [PMID: 35525551 DOI: 10.1016/bs.mie.2022.03.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HER3 is a potent oncogenic growth factor receptor belonging to the human epidermal growth factor (HER/EGFR) family of receptor tyrosine kinases. In contrast to other EGFR family members, HER3 is a pseudokinase, lacking functional kinase activity. As such, efforts to develop small molecule tyrosine kinase inhibitors against this family member have been limited. In response to HER3-specific growth factors such as neuregulin (NRG, also known as heregulin or HRG), HER3 must couple with catalytically active family members, including its preferred partner HER2. Dimerization of the intracellular HER2:HER3 kinase domains is a critical part of the activation mechanism and HER3 plays a specialized role as an allosteric activator of the active HER2 kinase partner. Intriguingly, many pseudokinases retain functionally important nucleotide binding capacity, despite loss of kinase activity. We demonstrated that occupation of the nucleotide pocket of the pseudokinase HER3 retains functional importance for growth factor signaling through oncogenic HER2:HER3 heterodimers. Mutation of the HER3 nucleotide pocket both disrupts signaling and disrupts HER2:HER3 dimerization. Conversely, ATP competitive drugs which bind to HER3, but not HER2, can stabilize HER2:HER3 dimers, induce signaling and promote cell growth in breast cancer models. This indicates a nucleotide-dependent conformational role for the HER3 kinase domain. Critically, our recent proof-of-concept work demonstrated that HER3-directed small molecule inhibitors can also disrupt HER2:HER3 dimerization and signaling, supporting the prospect that HER3 can be a direct drug target despite its lack of intrinsic activity. In this chapter we will describe methods for identifying and validating small molecule inhibitors against the HER3 pseudokinase.
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16
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Jain N, Sk MF, Mishra A, Kar P, Kumar A. Identification of novel Efflux pump inhibitors for Neisseria gonorrhoeae via multiple ligand-based pharmacophores, e-pharmacophore, molecular docking, density functional theory, and Molecular dynamics approaches. Comput Biol Chem 2022; 98:107682. [DOI: 10.1016/j.compbiolchem.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022]
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17
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Image-Based Annotation of Chemogenomic Libraries for Phenotypic Screening. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041439. [PMID: 35209227 PMCID: PMC8878468 DOI: 10.3390/molecules27041439] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/26/2022]
Abstract
Phenotypical screening is a widely used approach in drug discovery for the identification of small molecules with cellular activities. However, functional annotation of identified hits often poses a challenge. The development of small molecules with narrow or exclusive target selectivity such as chemical probes and chemogenomic (CG) libraries, greatly diminishes this challenge, but non-specific effects caused by compound toxicity or interference with basic cellular functions still pose a problem to associate phenotypic readouts with molecular targets. Hence, each compound should ideally be comprehensively characterized regarding its effects on general cell functions. Here, we report an optimized live-cell multiplexed assay that classifies cells based on nuclear morphology, presenting an excellent indicator for cellular responses such as early apoptosis and necrosis. This basic readout in combination with the detection of other general cell damaging activities of small molecules such as changes in cytoskeletal morphology, cell cycle and mitochondrial health provides a comprehensive time-dependent characterization of the effect of small molecules on cellular health in a single experiment. The developed high-content assay offers multi-dimensional comprehensive characterization that can be used to delineate generic effects regarding cell functions and cell viability, allowing an assessment of compound suitability for subsequent detailed phenotypic and mechanistic studies.
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18
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Bhurta D, Bharate SB. Styryl Group, a Friend or Foe in Medicinal Chemistry. ChemMedChem 2022; 17:e202100706. [PMID: 35166041 DOI: 10.1002/cmdc.202100706] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/12/2022] [Indexed: 11/10/2022]
Abstract
The styryl (Ph-CH=CH-R) group is widely represented in medicinally important compounds, including drugs, clinical candidates, and molecular probes as it positively impacts the lipophilicity, oral absorption, and biological activity. The analysis of matched molecular pairs (styryl vs. phenethyl, phenyl, methyl, H) for the biological activity indicates the superiority aspect of styryl compounds. However, the Michael acceptor site in the styryl group makes it amenable to the nucleophilic attack by biological nucleophiles and transformation to the toxic metabolites. One of the downsides of styryl compounds is isomerization that impacts the molecular conformation and directly affects biological activity. The impact of cis-trans isomerism and isosteric replacements on biological activity is exemplified. We also discuss the styryl group-bearing drugs, clinical candidates, and fluorescent probes. Overall, the present review reveals the utility of the styryl group in medicinal chemistry and drug discovery.
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Affiliation(s)
- Deendyal Bhurta
- Council of Scientific & Industrial Research Indian Institute of Integrative Medicine, Natural Products and medicinal chemistry, 180001, Jammu, INDIA
| | - Sandip Bibishan Bharate
- Indian Institute of Integrative Medicine CSIR, Natural Products & Medicinal Chemistry, Canal Road, 180001, Jammu, INDIA
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19
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Choo MZY, Chai CLL. Promoting GAINs (Give Attention to Limitations in Assays) over PAINs Alerts: no PAINS, more GAINs. ChemMedChem 2022; 17:e202100710. [PMID: 35146933 DOI: 10.1002/cmdc.202100710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/14/2022] [Indexed: 11/09/2022]
Abstract
Many concepts and guidelines in medicinal chemistry have been introduced to aid in successful drug discovery and development. An example is the concept of Pan-Assay Interference Compounds (PAINS) and the elimination of such nuisance compounds from high-throughput screening (HTS) libraries. PAINs, along with other guidelines in medicinal chemistry, are like double-edged swords. If used appropriately, they may be beneficial for drug discovery and development. However, rigid and blind use of such concepts can hinder productivity. In this perspective, we introduce GAINS (give attention to limitations in assays) and highlight its relevance for successful drug discovery.
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Affiliation(s)
- Malcolm Z Y Choo
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, Singapore, 117543, Singapore
| | - Christina L L Chai
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, Singapore, 117543, Singapore
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20
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Using filters in virtual screening: A comprehensive guide to minimize errors and maximize efficiency. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2022. [DOI: 10.1016/bs.armc.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Skoreński M, Sieńczyk M. The Fellowship of Privileged Scaffolds-One Structure to Inhibit Them All. Pharmaceuticals (Basel) 2021; 14:ph14111164. [PMID: 34832946 PMCID: PMC8622370 DOI: 10.3390/ph14111164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/22/2022] Open
Abstract
Over the past few years, the application of privileged structure has emerged as a powerful approach to the discovery of new biologically active molecules. Privileged structures are molecular scaffolds with binding properties to the range of different biological targets. Moreover, privileged structures typically exhibit good drug-like properties, thus assuring more drug-like properties of modified compound. Our main objective is to discuss the privileged structures used for the development of antiviral agents.
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22
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Eldhose B, Pandrala M, Xavier C, Mohamed AA, Srivastava S, Sunkara AD, Dobi A, Malhotra SV. New Selective Inhibitors of ERG Positive Prostate Cancer: ERGi-USU-6 Salt Derivatives. ACS Med Chem Lett 2021; 12:1703-1709. [PMID: 34790292 PMCID: PMC8591719 DOI: 10.1021/acsmedchemlett.1c00308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
![]()
Prostate
cancer is among the leading causes of cancer related death
of men in the United States. The ERG gene fusion
leading to overexpression of near full-length ERG transcript and protein represents most prevalent (50–65%)
prostate cancer driver gene alterations. The ERG oncoprotein overexpression
persists in approximately 35% of metastatic castration resistant prostate
cancers. Due to the emergence of eventual refractoriness to second-
and third-generation androgen axis-based inhibitors, there remains
a pressing need to develop drugs targeting other validated prostate
cancer drivers such as ERG. Here we report the new and more potent
ERG inhibitor ERGi-USU-6 developed by structure–activity studies
from the parental ERGi-USU. We have developed an improved procedure
for the synthesis of ERGi-USU-6 and identified a salt formulation
that further improves its activity in biological assays for selective
targeting of ERG harboring prostate cancer cells.
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Affiliation(s)
- Binil Eldhose
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817, United States
| | - Mallesh Pandrala
- Division of Radiation & Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Charles Xavier
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817, United States
| | - Ahmed A. Mohamed
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817, United States
| | - Shiv Srivastava
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
| | - Anu D. Sunkara
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
- Washington Adventist University, Takoma Park, Maryland 20912, United States
| | - Albert Dobi
- Center for Prostate Disease Research, Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20889, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817, United States
| | - Sanjay V. Malhotra
- Division of Radiation & Cancer Biology, Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California 94305, United States
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23
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Sun J, Zhong H, Wang K, Li N, Chen L. Gains from no real PAINS: Where 'Fair Trial Strategy' stands in the development of multi-target ligands. Acta Pharm Sin B 2021; 11:3417-3432. [PMID: 34900527 PMCID: PMC8642439 DOI: 10.1016/j.apsb.2021.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Compounds that selectively modulate multiple targets can provide clinical benefits and are an alternative to traditional highly selective agents for unique targets. High-throughput screening (HTS) for multitarget-directed ligands (MTDLs) using approved drugs, and fragment-based drug design has become a regular strategy to achieve an ideal multitarget combination. However, the unexpected presence of pan-assay interference compounds (PAINS) suspects in the development of MTDLs frequently results in nonspecific interactions or other undesirable effects leading to artefacts or false-positive data of biological assays. Publicly available filters can help to identify PAINS suspects; however, these filters cannot comprehensively conclude whether these suspects are "bad" or innocent. Additionally, these in silico approaches may inappropriately label a ligand as PAINS. More than 80% of the initial hits can be identified as PAINS by the filters if appropriate biochemical tests are not used resulting in false positive data that are unacceptable for medicinal chemists in manuscript peer review and future studies. Therefore, extensive offline experiments should be used after online filtering to discriminate "bad" PAINS and avoid incorrect evaluation of good scaffolds. We suggest that the use of "Fair Trial Strategy" to identify interesting molecules in PAINS suspects to provide certain structure‒function insight in MTDL development.
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Key Words
- AD, Alzheimer disease
- ALARM NMR, a La assay to detect reactive molecules by nuclear magnetic resonance
- Biochemical experiment
- CADD, computer-aided drug design technology
- CoA, coenzyme A
- EGFR, epidermal growth factor receptor
- Fair trial strategy
- GSH, glutathione
- HER2, human epidermal growth factor receptor 2
- HTS, high-throughput screening
- In silico filtering
- LC−MS, liquid chromatography−mass spectrometry
- MTDLs, multitarget-directed ligands
- Multitarget-directed ligands
- PAINS suspects
- PAINS, pan-assay interference compounds
- QSAR, quantitative structure–activity relationship
- ROS, radicals and oxygen reactive species
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Affiliation(s)
- Jianbo Sun
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Zhong
- Department of Pharmacology of Traditional Chinese Medicine, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kun Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Na Li
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li Chen
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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24
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Yin Y, Hu H, Yang Z, Xu H, Wu J. RealVS: Toward Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases. J Chem Inf Model 2021; 61:4924-4939. [PMID: 34619030 DOI: 10.1021/acs.jcim.1c01021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accurate modeling of compound bioactivities is essential for the virtual screening of drug leads. In real-world scenarios, pharmacists tend to choose from the top-k hit compounds ranked by predicted bioactivities from a large database with interest to continue wet experiments for drug discovery. Significant improvement of the precision of the top hits in ligand-based virtual screening of drug leads is more valuable than conventional schemes for accurately predicting the bioactivities of all compounds from a large database. Here, we proposed a new method, RealVS, to significantly improve the top hits' precision and learn interpretable key substructures associated with compound bioactivities. The features of RealVS involve the following points. (1) Abundant transferable information from the source domain was introduced for alleviating the insufficiency of inactive ligands associated with drug targets. (2) The adversarial domain alignment was adopted to fit the distribution of generated features of compounds from the training data set and that from the screening database for greater model generalization ability. (3) A novel objective function was proposed to simultaneously optimize the classification loss, regression loss, and adversarial loss, where most inactive ligands tend to be screened out before activity regression prediction. (4) Graph attention networks were adopted for learning key substructures associated with ligand bioactivities for better model interpretability. The results on a large number of benchmark data sets show that our method has significantly improved the precision of top hits under various k values in ligand-based virtual screening of drug leads from large compound databases, which is of great value in real-world scenarios. The web server of RealVS is freely available at noveldelta.com/RealVS for academic purposes, where virtual screening of hits from large compound databases is accessible.
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Affiliation(s)
- Yueming Yin
- College of Telecommunications and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Haifeng Hu
- College of Telecommunications and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Zhen Yang
- National Engineering Research Center of Communications and Networking, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Huajian Xu
- College of Telecommunications and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
| | - Jiansheng Wu
- School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210003, China
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25
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Computational investigation to identify potent inhibitors of the GTPase-Kirsten RAt sarcoma virus (K-Ras) mutants G12C and G12D. Comput Biol Med 2021; 139:104946. [PMID: 34715554 DOI: 10.1016/j.compbiomed.2021.104946] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 02/06/2023]
Abstract
K-Ras mutations are frequent in various cancer types, and according to recent research, K-Ras possesses four-drug targeting sites. This increased our interest in finding potential small molecule inhibitors with anticancer activity to treat K-Ras-driven cancers. We utilized integrated bioinformatic strategies, such as XP docking, MM-GBSA, cell-line cytotoxicity prediction, ADMET, and molecular simulation, to discover potential inhibitors of G12C and G12D mutants compared to sotorasib, which is a recent FDA-approved inhibitor of G12C. We identified compounds, such as flupentixol, amlodipine, and fluvoxamine, for the G12C mutant and paroxetine, flupentixol, and zuclopenthixol for the G12D mutant with significant inhibitory functions. All five compounds bound to the H95 cryptic groove of mutant K-Ras with high efficiency and, like sotorasib, retained a novel binding mechanism with additional hydrophobic interactions at the molecular level. Furthermore, the simulation studies suggested that the binding of flupentixol and amlodipine to G12C stabilizes switch I and switch II. In contrast, paroxetine and flupentixol to G12D showed a similar trend compared to sotorasib complexes. Thus, despite the very dynamic functionality of K-Ras switches I and II, the binding of shortlisted compounds is highly stable. Therefore, the reported study provides potential drug candidates for K-Ras inhibition that can be further developed with in vitro and in vivo evidence for targeted therapy.
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Hariono M, Hariyono P, Dwiastuti R, Setyani W, Yusuf M, Salin N, Wahab H. Potential SARS-CoV-2 3CLpro inhibitors from chromene, flavonoid and hydroxamic acid compound based on FRET assay, docking and pharmacophore studies. RESULTS IN CHEMISTRY 2021; 3:100195. [PMID: 34567959 PMCID: PMC8451405 DOI: 10.1016/j.rechem.2021.100195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022] Open
Abstract
This present study reports some natural products and one hydroxamic acid synthetic compound which were previously reported as matrix metalloproteinase-9 (MMP-9) inhibitors to be evaluated for their inhibition toward severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 3-chymotrypsin-like protease (3CLpro). This enzyme is one of the proteins responsible for this coronaviral replication. Two herbal methanolic extracts i.e., Averrhoa carambola leaves and Ageratum conyzoides aerial part demonstrate >50% inhibition at 1000 µg/mL. Interestingly, apigenin, one of flavonoids, demonstrates 92% inhibition at 250 µg/mL (925 µM) as well as hydroxamic acid compound, N-isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid (NNGH), which shows 69% inhibition at 100 µM. The in vitro results are supported by the docking studies revealing that the binding mode of both compounds is mainly by interacting with GLU166 residue in the hydrophobic pocket of the 3CLpro. Pharmacophore mapping further supported the results by confirming that the in vitro activities of both compounds are due to their pharmacophore features employing hydrogen bond acceptor (HBA), hydrogen bond donor (HBD) and hydrophobic. Gas Chromatography-Mass Spectrometry (GC–MS) analysis reported chromene compounds in Ageratum conyzoides aerial part methanolic extract are potential to be this enzyme inhibitor candidate. These all results reflect their potencies to be SARS-CoV-2 inhibitors through 3CLpro inhibition mechanism.
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Affiliation(s)
- Maywan Hariono
- Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Pandu Hariyono
- Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Rini Dwiastuti
- Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Wahyuning Setyani
- Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Muhammad Yusuf
- Chemistry Department, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jatinangor, Sumedang 45363, West Java, Indonesia
| | - Nurul Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institute of Biotechnology Malaysia, Halaman Bukit Gambir, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Habibah Wahab
- Pharmaceutical Technology Department, School of Pharmaceutical Sciences and USM-RIKEN Centre for Ageing Science (URICAS), Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
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Pinzi L, Tinivella A, Gagliardelli L, Beneventano D, Rastelli G. LigAdvisor: a versatile and user-friendly web-platform for drug design. Nucleic Acids Res 2021; 49:W326-W335. [PMID: 34023895 PMCID: PMC8262749 DOI: 10.1093/nar/gkab385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/19/2021] [Accepted: 04/27/2021] [Indexed: 12/17/2022] Open
Abstract
Although several tools facilitating in silico drug design are available, their results are usually difficult to integrate with publicly available information or require further processing to be fully exploited. The rational design of multi-target ligands (polypharmacology) and the repositioning of known drugs towards unmet therapeutic needs (drug repurposing) have raised increasing attention in drug discovery, although they usually require careful planning of tailored drug design strategies. Computational tools and data-driven approaches can help to reveal novel valuable opportunities in these contexts, as they enable to efficiently mine publicly available chemical, biological, clinical, and disease-related data. Based on these premises, we developed LigAdvisor, a data-driven webserver which integrates information reported in DrugBank, Protein Data Bank, UniProt, Clinical Trials and Therapeutic Target Database into an intuitive platform, to facilitate drug discovery tasks as drug repurposing, polypharmacology, target fishing and profiling. As designed, LigAdvisor enables easy integration of similarity estimation results with clinical data, thereby allowing a more efficient exploitation of information in different drug discovery contexts. Users can also develop customizable drug design tasks on their own molecules, by means of ligand- and target-based search modes, and download their results. LigAdvisor is publicly available at https://ligadvisor.unimore.it/.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.,Clinical and Experimental Medicine, PhD Program, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Luca Gagliardelli
- Department of Engineering "Enzo Ferrari", University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Domenico Beneventano
- Department of Engineering "Enzo Ferrari", University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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Redhead MA, Owen CD, Brewitz L, Collette AH, Lukacik P, Strain-Damerell C, Robinson SW, Collins PM, Schäfer P, Swindells M, Radoux CJ, Hopkins IN, Fearon D, Douangamath A, von Delft F, Malla TR, Vangeel L, Vercruysse T, Thibaut J, Leyssen P, Nguyen TT, Hull M, Tumber A, Hallett DJ, Schofield CJ, Stuart DI, Hopkins AL, Walsh MA. Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19. Sci Rep 2021; 11:13208. [PMID: 34168183 PMCID: PMC8225628 DOI: 10.1038/s41598-021-92416-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022] Open
Abstract
Effective agents to treat coronavirus infection are urgently required, not only to treat COVID-19, but to prepare for future outbreaks. Repurposed anti-virals such as remdesivir and human anti-inflammatories such as barcitinib have received emergency approval but their overall benefits remain unclear. Vaccines are the most promising prospect for COVID-19, but will need to be redeveloped for any future coronavirus outbreak. Protecting against future outbreaks requires the identification of targets that are conserved between coronavirus strains and amenable to drug discovery. Two such targets are the main protease (Mpro) and the papain-like protease (PLpro) which are essential for the coronavirus replication cycle. We describe the discovery of two non-antiviral therapeutic agents, the caspase-1 inhibitor SDZ 224015 and Tarloxotinib that target Mpro and PLpro, respectively. These were identified through extensive experimental screens of the drug repurposing ReFRAME library of 12,000 therapeutic agents. The caspase-1 inhibitor SDZ 224015, was found to be a potent irreversible inhibitor of Mpro (IC50 30 nM) while Tarloxotinib, a clinical stage epidermal growth factor receptor inhibitor, is a sub micromolar inhibitor of PLpro (IC50 300 nM, Ki 200 nM) and is the first reported PLpro inhibitor with drug-like properties. SDZ 224015 and Tarloxotinib have both undergone safety evaluation in humans and hence are candidates for COVID-19 clinical evaluation.
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Affiliation(s)
- Martin A Redhead
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK.
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Lennart Brewitz
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Amelia H Collette
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Sean W Robinson
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Patrick M Collins
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Philipp Schäfer
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Mark Swindells
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Chris J Radoux
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | | | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Tika R Malla
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Laura Vangeel
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000, Leuven, Belgium
| | - Tu-Trinh Nguyen
- Calibr, Scripps Research, 11119 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Mitchell Hull
- Calibr, Scripps Research, 11119 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anthony Tumber
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - David J Hallett
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory,, The Ineos Oxford Institute for Antimicrobial Research, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - David I Stuart
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, UK
| | - Andrew L Hopkins
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
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Makhaeva GF, Lushchekina SV, Kovaleva NV, Yu Astakhova T, Boltneva NP, Rudakova EV, Serebryakova OG, Proshin AN, Serkov IV, Trofimova TP, Tafeenko VA, Radchenko EV, Palyulin VA, Fisenko VP, Korábečný J, Soukup O, Richardson RJ. Amiridine-piperazine hybrids as cholinesterase inhibitors and potential multitarget agents for Alzheimer's disease treatment. Bioorg Chem 2021; 112:104974. [PMID: 34029971 DOI: 10.1016/j.bioorg.2021.104974] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/24/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023]
Abstract
We synthesized eleven new amiridine-piperazine hybrids 5a-j and 7 as potential multifunctional agents for Alzheimer's disease (AD) treatment by reacting N-chloroacetylamiridine with piperazines. The compounds displayed mixed-type reversible inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Conjugates were moderate inhibitors of equine and human BChE with negligible fluctuation in anti-BChE activity, whereas anti-AChE activity was substantially dependent on N4-substitution of the piperazine ring. Compounds with para-substituted aromatic moieties (5g, 5h, and bis-amiridine 7) had the highest anti-AChE activity in the low micromolar range. Top-ranked compound 5h, N-(2,3,5,6,7,8-hexahydro-1H-cyclopenta[b]quinolin-9-yl)-2-[4-(4-nitro-phenyl)-piperazin-1-yl]-acetamide, had an IC50 for AChE = 1.83 ± 0.03 μM (Ki = 1.50 ± 0.12 and αKi = 2.58 ± 0.23 μM). The conjugates possessed low activity against carboxylesterase, indicating a likely absence of unwanted drug-drug interactions in clinical use. In agreement with analysis of inhibition kinetics and molecular modeling studies, the lead compounds were found to bind effectively to the peripheral anionic site of AChE and displace propidium, indicating their potential to block AChE-induced β-amyloid aggregation. Similar propidium displacement activity was first shown for amiridine. Two compounds, 5c (R = cyclohexyl) and 5e (R = 2-MeO-Ph), exhibited appreciable antioxidant capability with Trolox equivalent antioxidant capacity values of 0.47 ± 0.03 and 0.39 ± 0.02, respectively. Molecular docking and molecular dynamics simulations provided insights into the structure-activity relationships for AChE and BChE inhibition, including the observation that inhibitory potencies and computed pKa values of hybrids were generally lower than those of the parent molecules. Predicted ADMET and physicochemical properties of conjugates indicated good CNS bioavailability and safety parameters comparable to those of amiridine and therefore acceptable for potential lead compounds at the early stages of anti-AD drug development.
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Affiliation(s)
- Galina F Makhaeva
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Sofya V Lushchekina
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia; Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow 119334, Russia
| | - Nadezhda V Kovaleva
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Tatiana Yu Astakhova
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow 119334, Russia
| | - Natalia P Boltneva
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Elena V Rudakova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Olga G Serebryakova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Alexey N Proshin
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Igor V Serkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Tatiana P Trofimova
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Victor A Tafeenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Eugene V Radchenko
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir A Palyulin
- Institute of Physiologically Active Compounds Russian Academy of Sciences, Chernogolovka 142432, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir P Fisenko
- I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow 119881, Russia
| | - Jan Korábečný
- Biomedical Research Centre, University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic
| | - Ondrej Soukup
- Biomedical Research Centre, University Hospital Hradec Kralove, 500 05 Hradec Kralove, Czech Republic
| | - Rudy J Richardson
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109 USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109 USA; Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA.
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30
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Bolz SN, Adasme MF, Schroeder M. Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes. J Chem Inf Model 2021; 61:2248-2262. [PMID: 33899463 DOI: 10.1021/acs.jcim.0c01227] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pan-assay interference compounds (PAINS) are promiscuous compound classes that produce false positive hits in high-throughput screenings. Yet, the mechanisms of PAINS activity are poorly understood. Although PAINS are often associated with protein reactivity, several recent studies have shown that they also mediate noncovalent interactions. Aiming at a deep understanding of PAINS promiscuity, we performed an analysis of the Protein Data Bank to characterize the binding modes of PAINS. We explored the binding mode conservation of 34 PAINS classes present in 871 ligands and among 517 protein targets. The two major findings of this work are the following: First, different PAINS classes exhibit different levels of binding mode conservation. Our novel classification of PAINS based on binding mode similarity enables a rational assessment of PAINS from a structural perspective. Second, PAINS classes with variable binding modes can bind with high affinity. The evaluation of noncovalent binding modes of PAINS-like compounds sheds light on the mechanisms of promiscuous binding. Our findings could facilitate the decisions on how to deal with PAINS and help scientists to understand why PAINS produce hits in their screenings.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
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31
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Ismaili L, Monnin J, Etievant A, Arribas RL, Viejo L, Refouvelet B, Soukup O, Janockova J, Hepnarova V, Korabecny J, Kucera T, Jun D, Andrys R, Musilek K, Baguet A, García-Frutos EM, De Simone A, Andrisano V, Bartolini M, de los Ríos C, Marco-Contelles J, Haffen E. (±)- BIGI-3h: Pentatarget-Directed Ligand combining Cholinesterase, Monoamine Oxidase, and Glycogen Synthase Kinase 3β Inhibition with Calcium Channel Antagonism and Antiaggregating Properties for Alzheimer's Disease. ACS Chem Neurosci 2021; 12:1328-1342. [PMID: 33797877 DOI: 10.1021/acschemneuro.0c00803] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Multitarget-directed ligands (MTDLs) are considered a promising therapeutic strategy to address the multifactorial nature of Alzheimer's disease (AD). Novel MTDLs have been designed as inhibitors of human acetylcholinesterases/butyrylcholinesterases, monoamine oxidase A/B, and glycogen synthase kinase 3β and as calcium channel antagonists via the Biginelli multicomponent reaction. Among these MTDLs, (±)-BIGI-3h was identified as a promising new hit compound showing in vitro balanced activities toward the aforementioned recognized AD targets. Additional in vitro studies demonstrated antioxidant effects and brain penetration, along with the ability to inhibit the aggregation of both τ protein and β-amyloid peptide. The in vivo studies have shown that (±)-BIGI-3h (10 mg/kg intraperitoneally) significantly reduces scopolamine-induced cognitive deficits.
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Affiliation(s)
- Lhassane Ismaili
- Neurosciences intégratives et cliniques EA 481, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Julie Monnin
- Neurosciences intégratives et cliniques EA 481, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Adeline Etievant
- Neurosciences intégratives et cliniques EA 481, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Raquel L. Arribas
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/Diego de León, 62, 28006 Madrid, Spain
- Instituto Teofilo Hernando, Universidad Autónoma de Madrid, C/Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | - Lucía Viejo
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/Diego de León, 62, 28006 Madrid, Spain
- Instituto Teofilo Hernando, Universidad Autónoma de Madrid, C/Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | - Bernard Refouvelet
- Neurosciences intégratives et cliniques EA 481, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Ondrej Soukup
- Biomedical Research Center, University Hospital Hradec Kralove, Czech Republic, University of Defence, 50003 Hradec Kralove, Czech Republic
| | - Jana Janockova
- Biomedical Research Center, University Hospital Hradec Kralove, Czech Republic, University of Defence, 50003 Hradec Kralove, Czech Republic
| | - Vendula Hepnarova
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, 66210 Brno, Czech Republic
| | - Jan Korabecny
- Biomedical Research Center, University Hospital Hradec Kralove, Czech Republic, University of Defence, 50003 Hradec Kralove, Czech Republic
| | - Tomas Kucera
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, 66210 Brno, Czech Republic
| | - Daniel Jun
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, 66210 Brno, Czech Republic
| | - Rudolf Andrys
- Faculty of Science, Department of Chemistry, University Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Faculty of Science, Department of Chemistry, University Hradec Kralove, Rokitanskeho 62, 50003 Hradec Kralove, Czech Republic
| | - Aurelie Baguet
- Université Bourgogne Franche Comté, INSERM, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France
| | - Eva M. García-Frutos
- Instituto de Ciencia de Materiales de Madrid, CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Angela De Simone
- Department for Life Quality Studies, Alma Mater Studiorum University of Bologna, Corso di Augusto, 237, 47921 Rimini, Italy
| | - Vincenza Andrisano
- Department for Life Quality Studies, Alma Mater Studiorum University of Bologna, Corso di Augusto, 237, 47921 Rimini, Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Cristóbal de los Ríos
- Servicio de Farmacología Clínica, Instituto de Investigación Sanitaria, Hospital Universitario de la Princesa, C/Diego de León, 62, 28006 Madrid, Spain
- Instituto Teofilo Hernando, Universidad Autónoma de Madrid, C/Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | - José Marco-Contelles
- Laboratory of Medicinal Chemistry, Instituto de Química Orgánica General, Consejo Superior de Investigaciones Científicas, Juan de la Cierva 3, 28006 Madrid, Spain
| | - Emmanuel Haffen
- Neurosciences intégratives et cliniques EA 481, Univ. Bourgogne Franche-Comté, F-25000 Besançon, France
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Täger J, Wissinger B, Kohl S, Reuter P. Identification of Chemical and Pharmacological Chaperones for Correction of Trafficking-Deficient Mutant Cyclic Nucleotide-Gated A3 Channels. Mol Pharmacol 2021; 99:460-468. [PMID: 33827965 DOI: 10.1124/molpharm.120.000180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Trafficking deficiency caused by missense mutations is a well known phenomenon that occurs for mutant, misfolded proteins. Typically, the misfolded protein is retained by the protein quality-control system and degraded by the endoplasmic reticulum-associated protein degradation pathway and thus does not reach its destination, although residual function of the protein may be preserved. Chemical and pharmacological chaperones can improve the targeting of trafficking-deficient proteins and thus may be promising candidates for therapeutic applications. Here, we report the application of a cellular bioassay based on the bioluminescent calcium reporter aequorin to quantify surface expression of mutant CNGA3 channels associated with the autosomal recessively inherited retinal disease achromatopsia. A screening of 77 compounds enabled the identification of effective chemical and pharmacological chaperones that result in a 1.5- to 4.8-fold increase of surface expression of mutant CNGA3. Using selected compounds, we confirmed that the rescue of the defective trafficking is not limited to a single mutation in CNGA3. Active compounds and our structure-activity correlated data for the dihydropyridine compound class may provide valuable information for developing a treatment of the trafficking defect in achromatopsia. SIGNIFICANCE STATEMENT: This study describes a novel luminescence-based assay to detect the surface expression of mutant trafficking-deficient CNGA3 channels based on the calcium-sensitive photoprotein aequorin. Using this assay for a compound screening, this study identifies novel chemical and pharmacological chaperones that restore the surface localization of mutant trafficking-deficient CNGA3 channels. The results from this work may serve as starting point for the development of potent compounds that rescue trafficking deficiencies in the autosomal recessively inherited retinal disease achromatopsia.
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Affiliation(s)
- Joachim Täger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
| | - Peggy Reuter
- Molecular Genetics Laboratory, Institute for Ophthalmic Research (J.T., B.W., S.K., P.R.), and Graduate School of Cellular and Molecular Neuroscience (J.T.), University of Tübingen, Tübingen, Germany
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Affiliation(s)
- Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
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Campora M, Canale C, Gatta E, Tasso B, Laurini E, Relini A, Pricl S, Catto M, Tonelli M. Multitarget Biological Profiling of New Naphthoquinone and Anthraquinone-Based Derivatives for the Treatment of Alzheimer's Disease. ACS Chem Neurosci 2021; 12:447-461. [PMID: 33428389 PMCID: PMC7880572 DOI: 10.1021/acschemneuro.0c00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
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Two
series of naphthoquinone and anthraquinone derivatives decorated
with an aromatic/heteroaromatic chain have been synthesized and evaluated
as potential promiscuous agents capable of targeting different factors
playing a key role in Alzheimer’s disease (AD) pathogenesis.
On the basis of the in vitro biological profiling,
most of them exhibited a significant ability to inhibit amyloid aggregation,
PHF6 tau sequence aggregation, acetylcholinesterase (AChE), and monoamine
oxidase (MAO) B. In particular, naphthoquinone 2 resulted
as one of the best performing multitarget-directed ligand (MTDL) experiencing
a high potency profile in inhibiting β-amyloid (Aβ40) aggregation (IC50 = 3.2 μM), PHF6 tau
fragment (91% at 10 μM), AChE enzyme (IC50 = 9.2
μM) jointly with a remarkable inhibitory activity against MAO
B (IC50 = 7.7 nM). Molecular modeling studies explained
the structure–activity relationship (SAR) around the binding
modes of representative compound 2 in complex with hMAO
B and hAChE enzymes, revealing inhibitor/protein key contacts and
the likely molecular rationale for enzyme selectivity. Compound 2 was also demonstrated to be a strong inhibitor of Aβ42 aggregation, with potency comparable to quercetin. Accordingly,
atomic force microscopy (AFM) revealed that the most promising naphthoquinones 2 and 5 and anthraquinones 11 and 12 were able to impair Aβ42 fibrillation,
deconstructing the morphologies of its fibrillar aggregates. Moreover,
the same compounds exerted a moderate neuroprotective effect against
Aβ42 toxicity in primary cultures of cerebellar granule
cells. Therefore, our findings demonstrate that these molecules may
represent valuable chemotypes toward the development of promising
candidates for AD therapy.
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Affiliation(s)
- Marta Campora
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Claudio Canale
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Elena Gatta
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Bruno Tasso
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
| | - Annalisa Relini
- Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), Department of Engineering and Architecture, University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
| | - Marco Catto
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV 3, 16132 Genoa, Italy
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Dey P. Low bioavailability hinders drug discovery against COVID-19, guided by in silico docking. Br J Pharmacol 2020; 178:741-742. [PMID: 33283265 DOI: 10.1111/bph.15325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/05/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022] Open
Affiliation(s)
- Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
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Chainoglou E, Siskos A, Pontiki E, Hadjipavlou-Litina D. Hybridization of Curcumin Analogues with Cinnamic Acid Derivatives as Multi-Target Agents Against Alzheimer's Disease Targets. Molecules 2020; 25:E4958. [PMID: 33114751 PMCID: PMC7662280 DOI: 10.3390/molecules25214958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
The synthesis of the new hybrids followed a hybridization with the aid of hydroxy-benzotriazole (HOBT) and 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDCI.HCL) in dry DMF or thionyl chloride between curcumin analogues and cinnamic acid derivatives. IR, 1H-NMR, 13C-NMR, LC/MS ESI+, and elemental analysis were used for the confirmation of the structures of the novel hybrids. The lipophilicity values of compounds were calculated theoretically and experimentally via the reversed chromatography method as RM values. The novel derivatives were studied through in vitro experiments for their activity as antioxidant agents and as inhibitors of lipoxygenase, cyclooxygenase-2, and acetyl-cholinesterase. All the compounds showed satisfying anti-lipid peroxidation activity of linoleic acid induced by 2,2'-azobis(2-amidinopropane) hydrochloride (AAPH). Hybrid 3e was the most significant pleiotropic derivative, followed by 3a. According to the predicted results, all hybrids could be easily transported, diffused, and absorbed through the blood-brain barrier (BBB). They presented good oral bioavailability and very high absorption with the exception of 3h. No inhibition for CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 was noticed. According to the Ames test, all the hybrids induced mutagenicity with the exception of 3d. Efforts were conducted a) to correlate the in vitro results with the most important physicochemical properties of the structural components of the molecules and b) to clarify the correlation of actions among them to propose a possible mechanism of action. Docking studies were performed on soybean lipoxygenase (LOX) and showed hydrophobic interactions with amino acids. Docking studies on acetylcholinesterase (AChE) exhibited: (a) hydrophobic interactions with TRP281, LEU282, TYR332, PHE333, and TYR336 and (b) π-stacking interactions with TYR336.
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Affiliation(s)
| | | | | | - Dimitra Hadjipavlou-Litina
- Department of Pharmaceutical Chemistry, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (E.C.); (A.S.); (E.P.)
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Goodwin S, Shahtahmassebi G, Hanley QS. Statistical models for identifying frequent hitters in high throughput screening. Sci Rep 2020; 10:17200. [PMID: 33057035 PMCID: PMC7560657 DOI: 10.1038/s41598-020-74139-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
High throughput screening (HTS) interrogates compound libraries to find those that are “active” in an assay. To better understand compound behavior in HTS, we assessed an existing binomial survivor function (BSF) model of “frequent hitters” using 872 publicly available HTS data sets. We found large numbers of “infrequent hitters” using this model leading us to reject the BSF for identifying “frequent hitters.” As alternatives, we investigated generalized logistic, gamma, and negative binomial distributions as models for compound behavior. The gamma model reduced the proportion of both frequent and infrequent hitters relative to the BSF. Within this data set, conclusions about individual compound behavior were limited by the number of times individual compounds were tested (1–1613 times) and disproportionate testing of some compounds. Specifically, most tests (78%) were on a 309,847-compound subset (17.6% of compounds) each tested ≥ 300 times. We concluded that the disproportionate retesting of some compounds represents compound repurposing at scale rather than drug discovery. The approach to drug discovery represented by these 872 data sets characterizes the assays well by challenging them with many compounds while each compound is characterized poorly with a single assay. Aggregating the testing information from each compound across the multiple screens yielded a continuum with no clear boundary between normal and frequent hitting compounds.
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Affiliation(s)
- Samuel Goodwin
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Golnaz Shahtahmassebi
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Quentin S Hanley
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
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Di Martino RMC, Pruccoli L, Bisi A, Gobbi S, Rampa A, Martinez A, Pérez C, Martinez-Gonzalez L, Paglione M, Di Schiavi E, Seghetti F, Tarozzi A, Belluti F. Novel Curcumin-Diethyl Fumarate Hybrid as a Dualistic GSK-3β Inhibitor/Nrf2 Inducer for the Treatment of Parkinson's Disease. ACS Chem Neurosci 2020; 11:2728-2740. [PMID: 32663009 PMCID: PMC8009478 DOI: 10.1021/acschemneuro.0c00363] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
![]()
Common
copathogenic factors, including oxidative stress and neuroinflammation,
are found to play a vital role in the development of neurodegenerative
disorders, including Alzheimer’s disease (AD) and Parkinson’s
disease (PD). Nowadays, owing to the multifactorial character of the
diseases, no effective therapies are available, thus underlying the
need for new strategies. Overexpression of the enzyme GSK-3β
and downregulation of the Nrf2/ARE pathway are responsible for a decrease
in antioxidant defense effects. These pieces of evidence underline
the usefulness of dual GSK-3β inhibitors/Nrf2 inducers. In this
regard, to design a dual modulator, the structures of a curcumin-based
analogue, as GSK-3β inhibitor, and a diethyl fumarate fragment,
as Nrf2 inducer, were combined. Among the hybrids, 5 and 6 proved to effectively inhibit GSK-3β, while 4 and 5 showed a marked ability to activate Nrf2
together to increase the neuronal resistance to oxidative stress.
These last pieces of evidence translated into specific neuroprotective
effects of 4 and 5 against PD pathological
events including neurotoxicity elicited by α-synuclein aggregates
and 6-hydroxydopamine. Hybrid 5 also showed neuroprotective
effects in a C. elegans model of PD where the activation
of GSK-3β is intimately involved in Nrf2 regulation. In summary, 5 emerged as an interesting multitarget derivative, valuable
to be exploited in a multitarget PD perspective.
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Affiliation(s)
- Rita Maria Concetta Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Letizia Pruccoli
- Department for Life Quality Studies, Alma Mater Studiorum - University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Ana Martinez
- Centro de Investigaciones Biologica, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Concepción Pérez
- Centro de Investigaciones Biologica, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Maria Paglione
- Department of Biology, Agriculture and Food Science, National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Elia Di Schiavi
- Department of Biology, Agriculture and Food Science, National Research Council (CNR), Institute of Biosciences and BioResources (IBBR), Via Pietro Castellino 111, 80131 Naples, Italy
| | - Francesca Seghetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum - University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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A novel scaffold to fight Pseudomonas aeruginosa pyocyanin production: early steps to novel antivirulence drugs. Future Med Chem 2020; 12:1489-1503. [PMID: 32772556 DOI: 10.4155/fmc-2019-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Although bacterial resistance is a growing concern worldwide, the development of antibacterial drugs has been steadily decreasing. One alternative to fight this issue relies on reducing the bacteria virulence without killing it. PhzS plays a pivotal role in pyocyanin production in Pseudomonas aeruginosa. Results: A total of 31 thiazolidinedione derivatives were evaluated as putative PhzS inhibitors, using thermo shift assays. Compounds that significantly shifted PhzS's Tm had their mode of inhibition (cofactor competitor) and affinity calculated by thermo shift assays as well. The most promising compound (E)-5-(4-((4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)methoxy)benzylidene)thiazolidine-2,4-dione had their affinity confirmed by microscale thermophoresis (Kd = 18 μM). Cellular assays suggest this compound reduces pyocyanin production in vitro, but does not affect P. aeruginosa viability. Conclusion: The first inhibitor of PhzS is described.
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Abstract
Active efflux of antibiotics preventing their accumulation to toxic intracellular concentrations contributes to clinically relevant multidrug resistance. Inhibition of active efflux potentiates antibiotic activity, indicating that efflux inhibitors could be used in combination with antibiotics to reverse drug resistance. Expression of ramA by Salmonella enterica serovar Typhimurium increases in response to efflux inhibition, irrespective of the mode of inhibition. We hypothesized that measuring ramA promoter activity could act as a reporter of efflux inhibition. A rapid, inexpensive, and high-throughput green fluorescent protein (GFP) screen to identify efflux inhibitors was developed, validated, and implemented. Two chemical compound libraries were screened for compounds that increased GFP production. Fifty of the compounds in the 1,200-compound Prestwick chemical library were identified as potential efflux inhibitors, including the previously characterized efflux inhibitors mefloquine and thioridazine. There were 107 hits from a library of 47,168 proprietary compounds from L. Hoffmann La Roche; 45 were confirmed hits, and a dose response was determined. Dye efflux and accumulation assays showed that 40 Roche and three Prestwick chemical library compounds were efflux inhibitors. Most compounds had specific efflux-inhibitor-antibiotic combinations and/or species-specific synergy in antibiotic disc diffusion and checkerboard assays performed with Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, and Salmonella Typhimurium. These data indicate that both narrow-spectrum and broad-spectrum combinations of efflux inhibitors with antibiotics can be found. Eleven novel efflux inhibitor compounds potentiated antibiotic activities against at least one species of Gram-negative bacteria, and data revealing an E. coli mutant with loss of AcrB function suggested that these are AcrB inhibitors.IMPORTANCE Multidrug-resistant Gram-negative bacteria pose a serious threat to human and animal health. Molecules that inhibit multidrug efflux offer an alternative approach to resolving the challenges caused by antibiotic resistance, by potentiating the activity of old, licensed, and new antibiotics. We have developed, validated, and implemented a high-throughput screen and used it to identify efflux inhibitors from two compound libraries selected for their high chemical and pharmacological diversity. We found that the new high-throughput screen is a valuable tool to identify efflux inhibitors, as evidenced by the 43 new efflux inhibitors described in this study.
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41
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Seghetti F, Di Martino RMC, Catanzaro E, Bisi A, Gobbi S, Rampa A, Canonico B, Montanari M, Krysko DV, Papa S, Fimognari C, Belluti F. Curcumin-1,2,3-Triazole Conjugation for Targeting the Cancer Apoptosis Machinery. Molecules 2020; 25:molecules25133066. [PMID: 32635622 PMCID: PMC7412087 DOI: 10.3390/molecules25133066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022] Open
Abstract
The burden of neoplastic diseases is widely recognized as a severe cause of mortality. The clinical inadequacy of most anticancer therapeutics urgently prompted intense drug discovery efforts toward the identification of new chemical entities endowed with a potent and safe antitumor profile. In this scenario, targeting cancer cells apoptosis machinery has emerged as a relevant strategy, useful for tackling the emergence of drug resistance. On this basis, a small library of naturally inspired hybrid molecules was obtained by combining, through a click chemistry approach, "privileged" synthons such as curcumin scaffold and 1,2,3-triazole building block. Compound 1, bearing a para-fluoro phenyl moiety, showed low-micromolar potency against T acute lymphoblastic leukemia cell growth. More in-depth biologic studies demonstrated, for this analog, cell death-inducing properties associated with its capability to simultaneously activate both the receptor and the mitochondrial apoptosis cascades. This peculiar behavior offers promises for achieving an expanded anticancer effect, namely intense cytotoxic response coupled with reduced predisposition of chemoresistance insurgence. Altogether, this study allowed the identification of compound 1 as a lead compound worth to be progressed as an anticancer drug candidate.
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Affiliation(s)
- Francesca Seghetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
| | - Rita Maria Concetta Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
| | - Elena Catanzaro
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy;
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via Ca’ Le Suore, 2, 61029 Urbino, Italy; (B.C.); (M.M.); (S.P.)
| | - Mariele Montanari
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via Ca’ Le Suore, 2, 61029 Urbino, Italy; (B.C.); (M.M.); (S.P.)
| | - Dmitri V. Krysko
- Cell Death Investigation and Therapy Laboratory, Department of Human Structure and Repair, Ghent University, 9000 Ghent, Belgium;
- Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), 119146 Moscow, Russia
| | - Stefano Papa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via Ca’ Le Suore, 2, 61029 Urbino, Italy; (B.C.); (M.M.); (S.P.)
| | - Carmela Fimognari
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso d’Augusto 237, 47921 Rimini, Italy;
- Correspondence: (C.F.); (F.B.); Tel.: +39-0541434658 (C.F.); Tel.: +39-0512099732 (F.B.)
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy; (F.S.); (R.M.C.D.M.); (A.B.); (S.G.); (A.R.)
- Correspondence: (C.F.); (F.B.); Tel.: +39-0541434658 (C.F.); Tel.: +39-0512099732 (F.B.)
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42
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Yang ZY, He JH, Lu AP, Hou TJ, Cao DS. Frequent hitters: nuisance artifacts in high-throughput screening. Drug Discov Today 2020; 25:657-667. [DOI: 10.1016/j.drudis.2020.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/28/2019] [Accepted: 01/16/2020] [Indexed: 11/27/2022]
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43
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Abstract
The privileged substructure (PS) and activity cliff (AC) concepts are popular in pharmaceutical research. PSs have been empirically identified as preferred building blocks for target-class-directed generation of active compounds. Although some PSs are controversially viewed, they continue to receive much attention in drug discovery. ACs are formed by structurally similar active compounds with large potency differences and thus capture structure-activity relationship (SAR) discontinuity and reveal SAR determinants. So far, the PS and AC concepts have not been investigated in context. We have systematically explored ACs formed by compounds containing different PSs (PS-ACs). Such ACs were frequently identified in different series of compounds. PS-ACs were thoroughly characterized and compared to ACs formed by other compounds. The analysis revealed differences in AC formation between PSs. For example, individual PSs with an unusually high proportion of AC-forming compounds were identified. Furthermore, PS-AC network analysis identified clusters of ACs containing the same PS in different compound structure contexts with activity against different targets. From such PS-AC clusters, target-specific SAR information for PSs in different structural environments can be extracted.
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Affiliation(s)
- Huabin Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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44
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Yang Y, Zhang Y, Hua Y, Chen X, Fan Y, Wang Y, Liang L, Deng C, Lu T, Chen Y, Liu H. In Silico Design and Analysis of a Kinase-Focused Combinatorial Library Considering Diversity and Quality. J Chem Inf Model 2020; 60:92-107. [PMID: 31886658 DOI: 10.1021/acs.jcim.9b00841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A structurally diverse, high-quality, and kinase-focused database plays a critical role in finding hits or leads in kinase drug discovery. Here, we propose a workflow for designing a virtual kinase-focused combinatorial library using existing structures. Based on the analysis of known protein kinase inhibitors (PKIs), detailed fragment optimization, fragment selection, fragment linking, and a molecular filtering scheme were defined. Quick recognition of core fragments that can possibly form dual hydrogen bonds with the hinge region of the ATP-pocket was proposed. Furthermore, three diversity and four quality metrics were chosen for compound library analysis, which can be applied to databases with over 30 million structures. Compared with 13 commercial libraries, our protocol demonstrates a special advantage in terms of good skeleton diversity, acceptable fingerprint diversity, balanced scaffold distribution, and high quality, which can work well not only on existing PKIs, but also on four chosen commercial libraries. Overall, the strategy can greatly facilitate the expansion of a desirable chemical space for kinase drug discovery.
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Affiliation(s)
- Yan Yang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Xingye Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuanrong Fan
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Yuchen Wang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Li Liang
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Chenglong Deng
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China.,State Key Laboratory of Natural Medicines , China Pharmaceutical University , 24 Tongjiaxiang , Nanjing 210009 , China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science , China Pharmaceutical University , 639 Longmian Avenue , Nanjing 211198 , China
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Li Y, Li W, Fu C, Song Y, Fu Q. Lonicerae japonicae flos and Lonicerae flos: a systematic review of ethnopharmacology, phytochemistry and pharmacology. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2020; 19:1-61. [PMID: 32206048 PMCID: PMC7088551 DOI: 10.1007/s11101-019-09655-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 11/11/2019] [Indexed: 05/05/2023]
Abstract
Lonicerae japonicae flos (called Jinyinhua, JYH in Chinese), flowers or flower buds of Lonicera japonica Thunberg, is an extremely used traditional edible-medicinal herb. Pharmacological studies have already proved JYH ideal clinical therapeutic effects on inflammation and infectious diseases and prominent effects on multiple targets in vitro and in vivo, such as pro-inflammatory protein inducible nitric oxide synthase, toll-like receptor 4, interleukin-1 receptor. JYH and Lonicerae flos [called Shanyinhua, SYH in Chinese, flowers or flower buds of Lonicera hypoglauca Miquel, Lonicera confusa De Candolle or Lonicera macrantha (D.Don) Spreng] which belongs to the same family of JYH were once recorded as same herb in multiple versions of Chinese Pharmacopoeia (ChP). However, they were listed as two different herbs in 2005 Edition ChP, leading to endless controversy since they have close proximity on plant species, appearances and functions, together with traditional applications. In the past decades, there has no literature regarding to systematical comparison on the similarity concerning research achievements of the two herbs. This review comprehensively presents similarities and differences between JYH and SYH retrospectively, particularly proposing them the marked differences in botanies, phytochemistry and pharmacological activities which can be used as evidence of separate list of JYH and SYH. Furthermore, deficiencies on present studies have also been discussed so as to further research could use for reference.
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Affiliation(s)
- Yuke Li
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 People’s Republic of China
| | - Wen Li
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 People’s Republic of China
| | - Chaomei Fu
- Pharmacy College of Chengdu University of Traditional Chinese Medicine, Chengdu, 611137 People’s Republic of China
| | - Ying Song
- Teaching Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610075 People’s Republic of China
| | - Qiang Fu
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106 People’s Republic of China
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46
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Pinzi L, Rastelli G. Identification of Target Associations for Polypharmacology from Analysis of Crystallographic Ligands of the Protein Data Bank. J Chem Inf Model 2019; 60:372-390. [PMID: 31800237 DOI: 10.1021/acs.jcim.9b00821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The design of a chemical entity that potently and selectively binds to a biological target of therapeutic relevance has dominated the scene of drug discovery so far. However, recent findings suggest that multitarget ligands may be endowed with superior efficacy and be less prone to drug resistance. The Protein Data Bank (PDB) provides experimentally validated structural information about targets and bound ligands. Therefore, it represents a valuable source of information to help identifying active sites, understanding pharmacophore requirements, designing novel ligands, and inferring structure-activity relationships. In this study, we performed a large-scale analysis of the PDB by integrating different ligand-based and structure-based approaches, with the aim of identifying promising target associations for polypharmacology based on reported crystal structure information. First, the 2D and 3D similarity profiles of the crystallographic ligands were evaluated using different ligand-based methods. Then, activity data of pairs of similar ligands binding to different targets were inspected by comparing structural information with bioactivity annotations reported in the ChEMBL, BindingDB, BindingMOAD, and PDBbind databases. Afterward, extensive docking screenings of ligands in the identified cross-targets were made in order to validate and refine the ligand-based results. Finally, the therapeutic relevance of the identified target combinations for polypharmacology was evaluated from comparison with information on therapeutic targets reported in the Therapeutic Target Database (TTD). The results led to the identification of several target associations with high therapeutic potential for polypharmacology.
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Affiliation(s)
- Luca Pinzi
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Giuseppe Campi 103 , 41125 Modena , Italy
| | - Giulio Rastelli
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Giuseppe Campi 103 , 41125 Modena , Italy
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47
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Identifying Promiscuous Compounds with Activity against Different Target Classes. Molecules 2019; 24:molecules24224185. [PMID: 31752252 PMCID: PMC6891533 DOI: 10.3390/molecules24224185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022] Open
Abstract
Compounds with multitarget activity are of high interest for polypharmacological drug discovery. Such promiscuous compounds might be active against closely related target proteins from the same family or against distantly related or unrelated targets. Compounds with activity against distinct targets are not only of interest for polypharmacology but also to better understand how small molecules might form specific interactions in different binding site environments. We have aimed to identify compounds with activity against drug targets from different classes. To these ends, a systematic analysis of public biological screening data was carried out. Care was taken to exclude compounds from further consideration that were prone to experimental artifacts and false positive activity readouts. Extensively assayed compounds were identified and found to contain molecules that were consistently inactive in all assays, active against a single target, or promiscuous. The latter included more than 1000 compounds that were active against 10 or more targets from different classes. These multiclass ligands were further analyzed and exemplary compounds were found in X-ray structures of complexes with distinct targets. Our collection of multiclass ligands should be of interest for pharmaceutical applications and further exploration of binding characteristics at the molecular level. Therefore, these highly promiscuous compounds are made publicly available.
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48
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Abstract
Aim: The druggability of epigenetic targets has prompted researchers to develop small-molecule therapeutics. However, no systematic assessment has ever been done to investigate the chemical space of epigenetic modulators. Herein, we report a comprehensive chemoinformatic analysis of epigenetic ligands from EpiDBase, HEMD, ChEMBL and PubChem databases. Results: Nearly, 0.45 × 106 ligands were analyzed for assay interference compounds, target profiling, drug-like properties and hit prioritization. After eliminating approximately 96,000 problematic compounds, the remaining 0.36 × 106 compounds were studied for their physicochemical distributions, principal component analysis and hit prioritization. More than 30% of assay interference compounds were determined for many proteins. Conclusion: This systematic assessment of epigenetic ligands will help in the enrichment of screening libraries with high-quality compounds and thus, the generation of efficacious drug candidates.
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Vásquez AF, González Barrios A. Pushing the Ligand Efficiency Metrics: Relative Group Contribution (RGC) Model as a Helpful Strategy to Promote a Fragment "Rescue" Effect. Front Chem 2019; 7:564. [PMID: 31482085 PMCID: PMC6710606 DOI: 10.3389/fchem.2019.00564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/24/2019] [Indexed: 12/30/2022] Open
Abstract
The ligand efficiency (LE) indexes have long been used as decision-making criteria in drug discovery and development. However, in the context of fragment-based drug design (FBDD), these metrics often exhibit a strong emphasis toward the selection of highly efficient “core” fragments for potential optimization, which are not usually considered as parts of a larger molecule with a size typical for a drug. In this study, we present a relative group contribution (RGC) model intended to predict the efficiency of a drug-sized compound in terms of its component fragments. This model could be useful not only in rapidly predicting all the possible combinations of promising fragments from an earlier hit discovery stage, but also in enabling a relatively low-LE fragment to become part of a drug-sized compound as long as it is “rescued” by other high-LE fragments.
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Affiliation(s)
- Andrés Felipe Vásquez
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia.,Laboratorio de Fisiología Molecular, Instituto Nacional de Salud, Bogotá, Colombia
| | - Andrés González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), School of Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
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50
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Dantas RF, Evangelista TCS, Neves BJ, Senger MR, Andrade CH, Ferreira SB, Silva-Junior FP. Dealing with frequent hitters in drug discovery: a multidisciplinary view on the issue of filtering compounds on biological screenings. Expert Opin Drug Discov 2019; 14:1269-1282. [DOI: 10.1080/17460441.2019.1654453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Rafael Ferreira Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tereza Cristina Santos Evangelista
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Junior Neves
- LabChem – Laboratory of Cheminformatics, Centro Universitário de Anápolis, UniEVANGÉLICA, Anápolis, Brazil
| | - Mario Roberto Senger
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina Horta Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, Brazil
| | - Sabrina Baptista Ferreira
- LaSOPB – Laboratório de Síntese Orgânica e Prospecção Biológica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Floriano Paes Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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