1
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Shu J, Wang Y, Guo W, Liu T, Cai S, Shi T, Hu W. Carbenoid-involved reactions integrated with scaffold-based screening generates a Nav1.7 inhibitor. Commun Chem 2024; 7:135. [PMID: 38866907 PMCID: PMC11169417 DOI: 10.1038/s42004-024-01213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
The discovery of selective Nav1.7 inhibitors is a promising approach for developing anti-nociceptive drugs. In this study, we present a novel oxindole-based readily accessible library (OREAL), which is characterized by readily accessibility, unique chemical space, ideal drug-like properties, and structural diversity. We used a scaffold-based approach to screen the OREAL and discovered compound C4 as a potent Nav1.7 inhibitor. The bioactivity characterization of C4 reveals that it is a selective Nav1.7 inhibitor and effectively reverses Paclitaxel-induced neuropathic pain (PINP) in rodent models. Preliminary toxicology study shows C4 is negative to hERG. The consistent results of molecular docking and molecular simulations further support the reasonability of the in-silico screening and show the insight of the binding mode of C4. Our discovery of C4 paves the way for pushing the Nav1.7-based anti-nociceptive drugs forward to the clinic.
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Affiliation(s)
- Jirong Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuwei Wang
- Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Weijie Guo
- Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Tao Liu
- Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Song Cai
- Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Taoda Shi
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Wenhao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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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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Zhang R, Wu C, Yang Q, Liu C, Wang Y, Li K, Huang L, Zhou F. MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning. Bioinformatics 2024; 40:btae118. [PMID: 38426310 PMCID: PMC10984949 DOI: 10.1093/bioinformatics/btae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/04/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
MOTIVATION Predicting molecular properties is a pivotal task in various scientific domains, including drug discovery, material science, and computational chemistry. This problem is often hindered by the lack of annotated data and imbalanced class distributions, which pose significant challenges in developing accurate and robust predictive models. RESULTS This study tackles these issues by employing pretrained molecular models within a few-shot learning framework. A novel dynamic contrastive loss function is utilized to further improve model performance in the situation of class imbalance. The proposed MolFeSCue framework not only facilitates rapid generalization from minimal samples, but also employs a contrastive loss function to extract meaningful molecular representations from imbalanced datasets. Extensive evaluations and comparisons of MolFeSCue and state-of-the-art algorithms have been conducted on multiple benchmark datasets, and the experimental data demonstrate our algorithm's effectiveness in molecular representations and its broad applicability across various pretrained models. Our findings underscore MolFeSCues potential to accelerate advancements in drug discovery. AVAILABILITY AND IMPLEMENTATION We have made all the source code utilized in this study publicly accessible via GitHub at http://www.healthinformaticslab.org/supp/ or https://github.com/zhangruochi/MolFeSCue. The code (MolFeSCue-v1-00) is also available as the supplementary file of this paper.
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Affiliation(s)
- Ruochi Zhang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- School of Artificial Intelligence, Jilin University, Changchun 130012, China
| | - Chao Wu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
| | - Qian Yang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
| | - Chang Liu
- Beijing Life Science Academy, Beijing 102209, China
| | - Yan Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
| | - Kewei Li
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
| | - Lan Huang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
| | - Fengfeng Zhou
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin 130012, China
- College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550025, China
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4
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Khodair AI, El-Hallouty SM, Cagle-White B, Abdel Aziz MH, Hanafy MK, Mowafy S, Hamdy NM, Kassab SE. Camptothecin structure simplification elaborated new imidazo[2,1-b]quinazoline derivative as a human topoisomerase I inhibitor with efficacy against bone cancer cells and colon adenocarcinoma. Eur J Med Chem 2024; 265:116049. [PMID: 38185054 DOI: 10.1016/j.ejmech.2023.116049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
Camptothecin is a pentacyclic natural alkaloid that inhibits the hTop1 enzyme involved in DNA transcription and cancer cell growth. Camptothecin structure pitfalls prompted us to design new congeners using a structure simplification strategy to reduce the ring extension number from pentacyclic to tetracyclic while maintaining potential stacking of the new compounds with the DNA base pairs at the Top1-mediated cleavage complex and aqueous solubility, as well as minimizing compound-liver toxicity. The principal axis of this study was the verification of hTop1 inhibiting activity as a possible mechanism of action and the elaboration of new simplified inhibitors with improved pharmacodynamic and pharmacokinetic profiling using three structure panels (A-C) of (isoquinolinoimidazoquinazoline), (imidazoquinazoline), and (imidazoisoquinoline), respectively. DNA relaxation assay identified five compounds as hTop1 inhibitors belonging to the imidazoisoquinolines 3a,b, the imidazoquinazolines 12, and the isoquinolinoimidazoquinazolines 7a,b. In an MTT cytotoxicity assay against different cancer cell lines, compound 12 was the most potent against HOS bone cancer cells (IC50 = 1.47 μM). At the same time, the other inhibitors had no detectable activity against any cancer cell type. Compound (12) demonstrated great penetrating power in the HOS cancer cells' 3D-multicellular tumor spheroid model. Bioinformatics research of the hTop1 gene revealed that the TP53 cell proliferative gene is in the network of hTop1. The finding is confirmed empirically using the gene expression assay that proved the increase in p53 expression. The impact of structure simplification on compound 12 profile, characterized by the absence of acute oral liver toxicity when compared to Doxorubicin as a standard inhibitor, the lethal dose measured on Swiss Albino female mice and reported at LD50 = 250 mg/kg, and therapeutic significance in reducing colon adenocarcinoma tumor volume by 75.36 % after five weeks of treatment with compound 12. The molecular docking solutions of the active CPT-based derivative 12 and the inactive congener 14 into the active site of hTop1 and the activity cliffing of such MMP directed us to recommend the addition of HBD and HBA variables to compound 12 imidazoquinazoline core scaffold to enhance the potency via hydrogen bond formation with the major groove amino acids (Asp533, Lys532) as well as maintaining the hydrogen bond with the minor groove amino acid Arg364.
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Affiliation(s)
- Ahmed I Khodair
- Chemistry Department, Faculty of Science, Kafrelsheikh University, 33516, Kafrelsheikh, Egypt.
| | - Salwa M El-Hallouty
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt
| | - Brittnee Cagle-White
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - May H Abdel Aziz
- Department of Pharmaceutical Sciences and Health Outcomes, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, TX 75799, USA
| | - Mahmoud Kh Hanafy
- Drug Bioassay-Cell Culture Laboratory, Department of Pharmacognosy, National Research Centre, Dokki, Giza 12622, Egypt; Research Centre for Idling Brain Science, Department of Biochemistry, Graduate School of Medicine and Pharmaceutical Science, University of Toyama, 930-0194, Japan
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt
| | - Nadia M Hamdy
- Biochemistry Dept., Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt.
| | - Shaymaa E Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt.
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5
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Redžepović I, Furtula B. Chemical similarity of molecules with physiological response. Mol Divers 2023; 27:1603-1612. [PMID: 35976549 DOI: 10.1007/s11030-022-10514-5] [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: 06/10/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Measuring the similarity among molecules is an important task in various chemically oriented problems. This elusive concept is hard to define and quantify. Moreover, the complexity of the problem is elevated by bifurcating the notion of molecular similarity to structural and chemical similarity. While the structural similarity of molecules is being extensively researched, the so-called chemical similarity is being mentioned scarcely. Here, we propose a way of converting the physico-chemical properties into molecular fingerprints. Then, using the apparatus of measuring the structural similarity, the chemical similarity can be assessed. The proof of a concept is demonstrated on a set of molecules that induce diverse physiological responses.
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Affiliation(s)
- Izudin Redžepović
- Department of Chemistry, Faculty of Science, University of Kragujevac, P. O. Box 60, 34000, Kragujevac, Serbia.
| | - Boris Furtula
- Department of Chemistry, Faculty of Science, University of Kragujevac, P. O. Box 60, 34000, Kragujevac, Serbia
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6
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Dablander M, Hanser T, Lambiotte R, Morris GM. Exploring QSAR models for activity-cliff prediction. J Cheminform 2023; 15:47. [PMID: 37069675 PMCID: PMC10107580 DOI: 10.1186/s13321-023-00708-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/10/2023] [Indexed: 04/19/2023] Open
Abstract
INTRODUCTION AND METHODOLOGY Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that QSAR models struggle to predict ACs and that ACs thus form a major source of prediction error. However, the AC-prediction power of modern QSAR methods and its quantitative relationship to general QSAR-prediction performance is still underexplored. We systematically construct nine distinct QSAR models by combining three molecular representation methods (extended-connectivity fingerprints, physicochemical-descriptor vectors and graph isomorphism networks) with three regression techniques (random forests, k-nearest neighbours and multilayer perceptrons); we then use each resulting model to classify pairs of similar compounds as ACs or non-ACs and to predict the activities of individual molecules in three case studies: dopamine receptor D2, factor Xa, and SARS-CoV-2 main protease. RESULTS AND CONCLUSIONS Our results provide strong support for the hypothesis that indeed QSAR models frequently fail to predict ACs. We observe low AC-sensitivity amongst the evaluated models when the activities of both compounds are unknown, but a substantial increase in AC-sensitivity when the actual activity of one of the compounds is given. Graph isomorphism features are found to be competitive with or superior to classical molecular representations for AC-classification and can thus be employed as baseline AC-prediction models or simple compound-optimisation tools. For general QSAR-prediction, however, extended-connectivity fingerprints still consistently deliver the best performance amongs the tested input representations. A potential future pathway to improve QSAR-modelling performance might be the development of techniques to increase AC-sensitivity.
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Affiliation(s)
- Markus Dablander
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Thierry Hanser
- Lhasa Limited, Granary Wharf House, 2 Canal Wharf, Leeds, LS11 5PS, UK
| | - Renaud Lambiotte
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter (550), Woodstock Road, Oxford, OX2 6GG, UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
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7
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Aldeghi M, Graff DE, Frey N, Morrone JA, Pyzer-Knapp EO, Jordan KE, Coley CW. Roughness of Molecular Property Landscapes and Its Impact on Modellability. J Chem Inf Model 2022; 62:4660-4671. [DOI: 10.1021/acs.jcim.2c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matteo Aldeghi
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - David E. Graff
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nathan Frey
- Lincoln Laboratory, Massachusetts Institute of Technology, Lexington, Massachusetts 02421, United States
| | - Joseph A. Morrone
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | | | - Kirk E. Jordan
- IBM Thomas J. Watson Research Center, Cambridge, Massachusetts 02142, United States
| | - Connor W. Coley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Victoria-Muñoz F, Sánchez-Cruz N, Medina-Franco JL, Lopez-Vallejo F. Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa. RSC Adv 2022; 12:6783-6790. [PMID: 35424595 PMCID: PMC8981735 DOI: 10.1039/d1ra08352j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/20/2022] [Indexed: 11/21/2022] Open
Abstract
There are molecular structural features that are key to defining the agonist or antagonist activity on LasR, RhlR and PqsR transcription factors, associated with quorum sensing in Pseudomonas aeruginosa.
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Affiliation(s)
- Felipe Victoria-Muñoz
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Farmacia, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Investigación en Productos Naturales Vegetales Bioactivos, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
| | - Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510 Mexico
| | - Fabian Lopez-Vallejo
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Departamento de Química, Grupo de Investigación en Productos Naturales Vegetales Bioactivos, Av. Cra 30 # 45-03, Bogotá D.C., 11001 Colombia
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9
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Naveja JJ, Vogt M. Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications. Molecules 2021; 26:5291. [PMID: 34500724 PMCID: PMC8433811 DOI: 10.3390/molecules26175291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 01/21/2023] Open
Abstract
Analogue series play a key role in drug discovery. They arise naturally in lead optimization efforts where analogues are explored based on one or a few core structures. However, it is much harder to accurately identify and extract pairs or series of analogue molecules in large compound databases with no predefined core structures. This methodological review outlines the most common and recent methodological developments to automatically identify analogue series in large libraries. Initial approaches focused on using predefined rules to extract scaffold structures, such as the popular Bemis-Murcko scaffold. Later on, the matched molecular pair concept led to efficient algorithms to identify similar compounds sharing a common core structure by exploring many putative scaffolds for each compound. Further developments of these ideas yielded, on the one hand, approaches for hierarchical scaffold decomposition and, on the other hand, algorithms for the extraction of analogue series based on single-site modifications (so-called matched molecular series) by exploring potential scaffold structures based on systematic molecule fragmentation. Eventually, further development of these approaches resulted in methods for extracting analogue series defined by a single core structure with several substitution sites that allow convenient representations, such as R-group tables. These methods enable the efficient analysis of large data sets with hundreds of thousands or even millions of compounds and have spawned many related methodological developments.
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Affiliation(s)
- José J. Naveja
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Martin Vogt
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5-6, 53115 Bonn, Germany
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10
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GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds. Sci Rep 2021; 11:9510. [PMID: 33947911 PMCID: PMC8097070 DOI: 10.1038/s41598-021-88939-5] [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: 04/05/2020] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
The current study describes the construction of various ligand-based machine learning models to be used for drug-repurposing against the family of G-Protein Coupled Receptors (GPCRs). In building these models, we collected > 500,000 data points, encompassing experimentally measured molecular association data of > 160,000 unique ligands against > 250 GPCRs. These data points were retrieved from the GPCR-Ligand Association (GLASS) database. We have used diverse molecular featurization methods to describe the input molecules. Multiple supervised ML algorithms were developed, tested and compared for their accuracy, F scores, as well as for their Matthews' correlation coefficient scores (MCC). Our data suggest that combined with molecular fingerprinting, ensemble decision trees and gradient boosted trees ML algorithms are on the accuracy border of the rather sophisticated deep neural nets (DNNs)-based algorithms. On a test dataset, these models displayed an excellent performance, reaching a ~ 90% classification accuracy. Additionally, we showcase a few examples where our models were able to identify interesting connections between known drugs from the Drug-Bank database and members of the GPCR family of receptors. Our findings are in excellent agreement with previously reported experimental observations in the literature. We hope the models presented in this paper synergize with the currently ongoing interest of applying machine learning modeling in the field of drug repurposing and computational drug discovery in general.
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11
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Prieto-Martínez FD, Medina-Franco JL. Current advances on the development of BET inhibitors: insights from computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:127-180. [PMID: 32951810 DOI: 10.1016/bs.apcsb.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Epigenetics was coined almost 70 years ago for the description of heritable phenotype without altering DNA sequences. Research on the field has uncovered significant roles of such mechanisms, that account for the biogenesis of several diseases. Further studies have led the way for drug development which targets epi-enzymes, mainly for cancer treatment. Of the numerous epi-targets involved with histone acetylation, bromodomains have captured the spotlight of drug discovery focused on novel therapies. However, due to high sequence identity, the development of potent and selective inhibitors poses a significant challenge. Herein, we discuss recent computational developments on BET inhibitors and other methods that may be applied for drug discovery in general. As a proof-of-concept, we discuss a virtual screening to identify novel BET inhibitors based on coumarin derivatives. From public data, we identified putative structure-activity relationships of coumarin scaffold and propose R-group modifications for BET selectivity. Results showed that the optimization and design of novel coumarins could be further explored.
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Affiliation(s)
- Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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12
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López-López E, Barrientos-Salcedo C, Prieto-Martínez FD, Medina-Franco JL. In silico tools to study molecular targets of neglected diseases: inhibition of TcSir2rp3, an epigenetic enzyme of Trypanosoma cruzi. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:203-229. [PMID: 32951812 DOI: 10.1016/bs.apcsb.2020.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a growing interest to study and address neglected tropical diseases (NTD). To this end, in silico methods can serve as the bridge that connects academy and industry, encouraging the development of future treatments against these diseases. This chapter discusses current challenges in the development of new therapies, available computational methods and successful cases in computer-aided design with particular focus on human trypanosomiasis. Novel targets are also discussed. As a case study, we identify amentoflavone as a potential inhibitor of TcSir2rp3 (sirtuine) from Trypanosoma cruzi (20.03 μM) with a workflow that integrates chemoinformatic approaches, molecular modeling, and theoretical affinity calculations, as well as in vitro assays.
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Affiliation(s)
- Edgar López-López
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico; Department of Pharmacology, Center of Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), Mexico City, Mexico
| | | | - Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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13
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Hu H, Bajorath J. Simplified activity cliff network representations with high interpretability and immediate access to SAR information. J Comput Aided Mol Des 2020; 34:943-952. [PMID: 32500478 PMCID: PMC7367913 DOI: 10.1007/s10822-020-00319-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/29/2020] [Indexed: 11/30/2022]
Abstract
Activity cliffs (ACs) consist of structurally similar compounds with a large difference in potency against their target. Accordingly, ACs introduce discontinuity in structure-activity relationships (SARs) and are a prime source of SAR information. In compound data sets, the vast majority of ACs are formed by differently sized groups of structurally similar compounds with large potency variations. As a consequence, many of these compounds participate in multiple ACs. This coordinated formation of ACs increases their SAR information content compared to ACs considered as individual compound pairs, but complicates AC analysis. In network representations, coordinated ACs give rise to clusters of varying size and topology, which can be interactively and computationally analyzed. While AC networks are indispensable tools to study coordinated ACs, they become difficult to navigate and interpret in the presence of clusters of increasing size and complex topologies. Herein, we introduce reduced network representations that transform AC networks into an easily interpretable format from which SAR information in the form of R-group tables can be readily obtained. The simplified network variant greatly improves the interpretability of large and complex AC networks and substantially supports SAR exploration.
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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, 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, 53115, Bonn, Germany.
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14
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Zhang H, Liu CT, Mao J, Shen C, Xie RL, Mu B. Development of novel in silico prediction model for drug-induced ototoxicity by using naïve Bayes classifier approach. Toxicol In Vitro 2020; 65:104812. [DOI: 10.1016/j.tiv.2020.104812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 02/23/2020] [Accepted: 02/24/2020] [Indexed: 12/23/2022]
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15
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Hu H, Bajorath J. Increasing the public activity cliff knowledge base with new categories of activity cliffs. Future Sci OA 2020; 6:FSO472. [PMID: 32518687 PMCID: PMC7273365 DOI: 10.2144/fsoa-2020-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aim: Extending the public knowledge base of activity cliffs (ACs) with new categories of ACs having special structural characteristics. Methodology: Dual-site ACs, isomer ACs and ACs with privileged substructures are described and their systematic identification is detailed. Exemplary results & data: More than 7400 new ACs belonging to different categories with activity against more than 200 targets were identified and are made publicly available. Limitations & next steps: For dual-site ACs, limited numbers of isomers are available as structural analogs for rationalizing contributions to AC formation. The search for such analogs will continue. In addition, the target distribution of ACs containing privileged substructures will be further analyzed. Activity cliffs (ACs) are formed by small molecules that have very similar structures, are active against the same biological target, but have a large difference in potency against their target. Accordingly, ACs are of interest in medicinal chemistry because they reveal small structural changes that greatly influence the potency of active compounds. This information can be used for compound optimization. Computational methods are applied to search for ACs in large compound databases. Here, we further extend the public AC knowledge base with new categories of ACs having special structural characteristics.
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Affiliation(s)
- Huabin Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, Bonn D-53113, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology & Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, Bonn D-53113, Germany
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16
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Martinez-Mayorga K, Madariaga-Mazon A, Medina-Franco JL, Maggiora G. The impact of chemoinformatics on drug discovery in the pharmaceutical industry. Expert Opin Drug Discov 2020; 15:293-306. [PMID: 31965870 DOI: 10.1080/17460441.2020.1696307] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Introduction: Even though there have been substantial advances in our understanding of biological systems, research in drug discovery is only just now beginning to utilize this type of information. The single-target paradigm, which exemplifies the reductionist approach, remains a mainstay of drug research today. A deeper view of the complexity involved in drug discovery is necessary to advance on this field.Areas covered: This perspective provides a summary of research areas where cheminformatics has played a key role in drug discovery, including of the available resources as well as a personal perspective of the challenges still faced in the field.Expert opinion: Although great strides have been made in the handling and analysis of biological and pharmacological data, more must be done to link the data to biological pathways. This is crucial if one is to understand how drugs modify disease phenotypes, although this will involve a shift from the single drug/single target paradigm that remains a mainstay of drug research. Moreover, such a shift would require an increased awareness of the role of physiology in the mechanism of drug action, which will require the introduction of new mathematical, computer, and biological methods for chemoinformaticians to be trained in.
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Affiliation(s)
| | | | - José L Medina-Franco
- Facultad de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
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17
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Zhang H, Mao J, Qi HZ, Ding L. In silico prediction of drug-induced developmental toxicity by using machine learning approaches. Mol Divers 2019; 24:1281-1290. [PMID: 31486961 DOI: 10.1007/s11030-019-09991-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/28/2019] [Indexed: 02/05/2023]
Abstract
Some drugs and xenobiotics have the potential to disturb homeostasis, normal growth, differentiation, development or behavior during prenatal development or postnatally until puberty. Assessment of the developmental toxicity is one of the important safety considerations incorporated by international regulatory agencies. In this investigation, seven machine learning methods, including naïve Bayes, support vector machine, recursive partitioning, k-nearest neighbor, C4.5 decision tree, random forest and Adaboost, were used to build binary classification models for developmental toxicity. Among these models, the naïve Bayes classifier represented the best predictive performance and stability, which gave 91.11% overall prediction accuracy, 91.50% balanced accuracy and 0.818 MCC for the training set, and generated 83.93% concordance, 81.85% balanced accuracy and 0.627 MCC for the test set. The application domains were analyzed, and only one chemical in the test set was identified as outside the application domain. In addition, 10 important molecular descriptors related to developmental toxicity were selected by the genetic algorithm, which may contribute to explanation of the mechanisms of developmental toxicants. The best naïve Bayes classification model should be employed as alternative method for qualitative prediction of chemical-induced developmental toxicity in early stages of drug development.
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Affiliation(s)
- Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China. .,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
| | - Jun Mao
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Hua-Zhao Qi
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China
| | - Lan Ding
- College of Life Science, Northwest Normal University, Lanzhou, 730070, Gansu, People's Republic of China.
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18
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Madhukar G, Malik MZ, Subbarao N. Development and rigorous validation of antimalarial predictive models using machine learning approaches. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:543-560. [PMID: 31328578 DOI: 10.1080/1062936x.2019.1635526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
The large collection of known and experimentally verified compounds from the ChEMBL database was used to build different classification models for predicting the antimalarial activity against Plasmodium falciparum. Four different machine learning methods, namely the support vector machine (SVM), random forest (RF), k-nearest neighbour (kNN) and XGBoost have been used for the development of models using the diverse antimalarial dataset from ChEMBL. A well-established feature selection framework was used to select the best subset from a larger pool of descriptors. Performance of the models was rigorously evaluated by evaluation of the applicability domain, Y-scrambling and AUC-ROC curve. Additionally, the predictive power of the models was also assessed using probability calibration and predictiveness curves. SVM and XGBoost showed the best performances, yielding an accuracy of ~85% on the independent test set. In term of probability prediction, SVM and XGBoost were well calibrated. Total gain (TG) from the predictiveness curve was more related to SVM (TG = 0.67) and XGBoost (TG = 0.75). These models also predict the high-affinity compounds from PubChem antimalarial bioassay (as external validation) with a high probability score. Our findings suggest that the selected models are robust and can be potentially useful for facilitating the discovery of antimalarial agents.
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Affiliation(s)
- G Madhukar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi , India
| | - M Z Malik
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi , India
| | - N Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University , New Delhi , India
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19
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Peón A, Li H, Ghislat G, Leung KS, Wong MH, Lu G, Ballester PJ. MolTarPred: A web tool for comprehensive target prediction with reliability estimation. Chem Biol Drug Des 2019; 94:1390-1401. [PMID: 30916462 DOI: 10.1111/cbdd.13516] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/07/2019] [Accepted: 03/03/2019] [Indexed: 12/17/2022]
Abstract
Molecular target prediction can provide a starting point to understand the efficacy and side effects of phenotypic screening hits. Unfortunately, the vast majority of in silico target prediction methods are not available as web tools. Furthermore, these are limited in the number of targets that can be predicted, do not estimate which target predictions are more reliable and/or lack comprehensive retrospective validations. We present MolTarPred ( http://moltarpred.marseille.inserm.fr/), a user-friendly web tool for predicting protein targets of small organic compounds. It is powered by a large knowledge base comprising 607,659 compounds and 4,553 macromolecular targets collected from the ChEMBL database. In about 1 min, the predicted targets for the supplied molecule will be listed in a table. The chemical structures of the query molecule and the most similar compounds annotated with the predicted target will also be shown to permit visual inspection and comparison. Practical examples of the use of MolTarPred are showcased. MolTarPred is a new resource for scientists that require a more complete knowledge of the polypharmacology of a molecule. The introduction of a reliability score constitutes an attractive functionality of MolTarPred, as it permits focusing experimental confirmatory tests on the most reliable predictions, which leads to higher prospective hit rates.
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Affiliation(s)
- Antonio Peón
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068, Inserm, Marseille, France.,UMR7258, CNRS, Marseille, France.,Institut Paoli-Calmettes, Marseille, France.,UM 105, Aix-Marseille University, Marseille, France
| | - Hongjian Li
- SDIVF R&D Centre, Hong Kong Science Park, Sha Tin, New Territories, Hong Kong.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Pedro J Ballester
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068, Inserm, Marseille, France.,UMR7258, CNRS, Marseille, France.,Institut Paoli-Calmettes, Marseille, France.,UM 105, Aix-Marseille University, Marseille, France
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20
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Martínez R, Zamudio GJN, Pretelin-Castillo G, Torres-Ochoa RO, Medina-Franco JL, Espitia Pinzón CI, Miranda MS, Hernández E, Alanís-Garza B. Synthesis and antitubercular activity of new N-[5-(4-chlorophenyl)-1,3,4-oxadiazol-2-yl]-(nitroheteroaryl)carboxamides. HETEROCYCL COMMUN 2019. [DOI: 10.1515/hc-2019-0007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractNitro-substituted heteroaromatic carboxamides 1a-e were synthesized and tested against three Mycobacterium tuberculosis cell lines. The activities can be explained in terms of the distribution of the electronic density across the nitro-substituted heteroaromatic ring attached to the amide group. 1,3,5-Oxadiazole derivatives 1c-e are candidates for the development of novel antitubercular agents. Ongoing studies are focused on exploring the mechanism by which these compounds inhibit M. tuberculosis cell growth.
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Affiliation(s)
- Roberto Martínez
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Cd. México, México
| | - Gladys J. Nieves Zamudio
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Cd. México, México
| | - Gustavo Pretelin-Castillo
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Cd. México, México
| | - Rubén O. Torres-Ochoa
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Cd. México, México
| | - José L. Medina-Franco
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Avenida Universidad3000, 04510Cd. México, México
| | - Clara I. Espitia Pinzón
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, México
| | - Mayra Silva Miranda
- Catedrática CONACYT adscrita al Insituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Cd. México, México
| | - Eugenio Hernández
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Pedro de Alba s/n, Ciudad Universitaria, 66400 San Nicolás de los Garza, Nuevo León, México
| | - Blanca Alanís-Garza
- Departamento de Química Analítica, Facultad de Medicina, Universidad Autónoma de Nuevo León, Madero s/n Col. Mitras Centro. Monterrey, N. L. MéxicoC. P. 64460
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21
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Zhang H, Ren JX, Ma JX, Ding L. Development of an in silico prediction model for chemical-induced urinary tract toxicity by using naïve Bayes classifier. Mol Divers 2018; 23:381-392. [DOI: 10.1007/s11030-018-9882-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/25/2018] [Indexed: 12/16/2022]
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22
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Capoferri L, van Dijk M, Rustenburg AS, Wassenaar TA, Kooi DP, Rifai EA, Vermeulen NPE, Geerke DP. eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. J Cheminform 2017; 9:58. [PMID: 29159598 PMCID: PMC5696310 DOI: 10.1186/s13321-017-0243-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/01/2017] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up the drug discovery process. However, use of ligand-based approaches can lead to erroneous predictions when structural and dynamic features of the target substantially affect ligand binding. Free energy methods for affinity computation can include steric and electrostatic protein-ligand interactions, solvent effects, and thermal fluctuations, but often they are computationally demanding and require a high level of supervision. As a result their application is typically limited to the screening of small sets of compounds by experts in molecular modeling. RESULTS We have developed eTOX ALLIES, an open source framework that allows the automated prediction of ligand-binding free energies requiring the ligand structure as only input. eTOX ALLIES is based on the linear interaction energy approach, an efficient end-point free energy method derived from Free Energy Perturbation theory. Upon submission of a ligand or dataset of compounds, the tool performs the multiple steps required for binding free-energy prediction (docking, ligand topology creation, molecular dynamics simulations, data analysis), making use of external open source software where necessary. Moreover, functionalities are also available to enable and assist the creation and calibration of new models. In addition, a web graphical user interface has been developed to allow use of free-energy based models to users that are not an expert in molecular modeling. CONCLUSIONS Because of the user-friendliness, efficiency and free-software licensing, eTOX ALLIES represents a novel extension of the toolbox for computational chemists, pharmaceutical scientists and toxicologists, who are interested in fast affinity predictions of small molecules toward biological (off-)targets for which protein flexibility, solvent and binding site interactions directly affect the strength of ligand-protein binding.
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Affiliation(s)
- Luigi Capoferri
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Marc van Dijk
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Ariën S. Rustenburg
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Present Address: Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Tsjerk A. Wassenaar
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Present Address: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Derk P. Kooi
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Eko A. Rifai
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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23
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Paguigan ND, Al-Huniti MH, Raja HA, Czarnecki A, Burdette JE, González-Medina M, Medina-Franco JL, Polyak SJ, Pearce CJ, Croatt MP, Oberlies NH. Chemoselective fluorination and chemoinformatic analysis of griseofulvin: Natural vs fluorinated fungal metabolites. Bioorg Med Chem 2017; 25:5238-5246. [PMID: 28802670 PMCID: PMC5632135 DOI: 10.1016/j.bmc.2017.07.041] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023]
Abstract
Griseofulvin is a fungal metabolite and antifungal drug used for the treatment of dermatophytosis in both humans and animals. Recently, griseofulvin and its analogues have attracted renewed attention due to reports of their potential anticancer effects. In this study griseofulvin (1) and related analogues (2-6, with 4 being new to literature) were isolated from Xylaria cubensis. Six fluorinated analogues (7-12) were synthesized, each in a single step using the isolated natural products and Selectflour, so as to examine the effects of fluorine incorporation on the bioactivities of this structural class. The isolated and synthesized compounds were screened for activity against a panel of cancer cell lines (MDA-MB-435, MDA-MB-231, OVCAR3, and Huh7.5.1) and for antifungal activity against Microsporum gypseum. A comparison of the chemical space occupied by the natural and fluorinated analogues was carried out by using principal component analysis, documenting that the isolated and fluorinated analogues occupy complementary regions of chemical space. However, the most active compounds, including two fluorinated derivatives, were centered around the chemical space that was occupied by the parent compound, griseofulvin, suggesting that modifications must preserve certain attributes of griseofulvin to conserve its activity.
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Affiliation(s)
- Noemi D Paguigan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Mohammed H Al-Huniti
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Austin Czarnecki
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Joanna E Burdette
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Mariana González-Medina
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Stephen J Polyak
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98104, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Cedric J Pearce
- Mycosynthetix Inc., 505 Meadowlands Drive, Suite 103, Hillsborough, NC 27278, USA
| | - Mitchell P Croatt
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, USA.
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González-Medina M, Méndez-Lucio O, Medina-Franco JL. Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships. J Chem Inf Model 2017; 57:397-402. [PMID: 28234475 DOI: 10.1021/acs.jcim.6b00776] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Activity landscape modeling is a powerful method for the quantitative analysis of structure-activity relationships. This cheminformatics area is in continuous growth, and several quantitative and visual approaches are constantly being developed. However, these approaches often fall into disuse due to their limited access. Herein, we present Activity Landscape Plotter as the first freely available web-based tool to automatically analyze structure-activity relationships of compound data sets. Based on the concept of activity landscape modeling, the online service performs pairwise structure and activity relationships from an input data set supplied by the user. For visual analysis, Activity Landscape Plotter generates Structure-Activity Similarity and Dual-Activity Difference maps. The user can interactively navigate through the maps and export all the pairwise structure-activity information as comma delimited files. Activity Landscape Plotter is freely accessible at https://unam-shiny-difacquim.shinyapps.io/ActLSmaps /.
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Affiliation(s)
- Mariana González-Medina
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Oscar Méndez-Lucio
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
| | - José L Medina-Franco
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
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25
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González-Medina M, Naveja JJ, Sánchez-Cruz N, Medina-Franco JL. Open chemoinformatic resources to explore the structure, properties and chemical space of molecules. RSC Adv 2017. [DOI: 10.1039/c7ra11831g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Open chemoinformatic servers facilitate analysis of chemical space and structure–activity relationships.
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Affiliation(s)
- Mariana González-Medina
- Department of Pharmacy
- School of Chemistry
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - J. Jesús Naveja
- Department of Pharmacy
- School of Chemistry
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - Norberto Sánchez-Cruz
- Department of Pharmacy
- School of Chemistry
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
| | - José L. Medina-Franco
- Department of Pharmacy
- School of Chemistry
- Universidad Nacional Autónoma de México
- Mexico City 04510
- Mexico
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26
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García-Jacas CR, Martinez-Mayorga K, Marrero-Ponce Y, Medina-Franco JL. Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:41-58. [PMID: 28161994 DOI: 10.1080/1062936x.2017.1278616] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/22/2016] [Indexed: 06/06/2023]
Abstract
Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented. A conformation-dependent representation of the chemical structures was established using the RDKit software and a training and test set division was performed. Several two-linear and three-linear QuBiLS-MIDAS molecular descriptors ( www.tomocomd.com ) were computed to extract the geometric structural features of the compounds studied. QuBiLS-MIDAS-based features sets, to be used in the modelling, were selected using dimensionality reduction strategies. The multiple linear regression procedure coupled with a genetic algorithm were employed to build the predictive models. Regression models containing between 6 to 9 variables were developed and assessed according to several internal and external validation methods. Analyses of outlier compounds and the applicability domain for each model were performed. As a result, the models against BRD2 and BRD3 with 8 variables and the model with 9 variables against BRD4 were those with the best overall performance according to the criteria accounted for. The results obtained suggest that the models proposed will be a good tool for studying the inhibitory activities of drug candidates against the bromodomains considered during epigenetic drug discovery.
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Affiliation(s)
- C R García-Jacas
- a Instituto de Química, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , México
- b Escuela de Sistemas y Computación , Pontificia Universidad Católica del Ecuador Sede Esmeraldas (PUCESE) , Esmeraldas , Ecuador
- c Grupo de Investigación de Bioinformática , Universidad de las Ciencias Informáticas (UCI) , La Habana , Cuba
| | - K Martinez-Mayorga
- a Instituto de Química, Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , México
| | - Y Marrero-Ponce
- d Grupo de Medicina Molecular y Traslacional (MeM&T) , Universidad San Francisco de Quito (USFQ) , Quito , Ecuador
- e Grupo de Investigación Ambiental (GIA) , Fundación Universitaria Tecnológica de Comfenalco , Bolívar , Colombia
| | - J L Medina-Franco
- f Departamento de Farmacia , Universidad Nacional Autónoma de México (UNAM) , Ciudad de México , México
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27
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García-Sánchez MO, Cruz-Monteagudo M, Medina-Franco JL. Quantitative Structure-Epigenetic Activity Relationships. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2017. [DOI: 10.1007/978-3-319-56850-8_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Peón A, Dang CC, Ballester PJ. How Reliable Are Ligand-Centric Methods for Target Fishing? Front Chem 2016; 4:15. [PMID: 27148522 PMCID: PMC4830838 DOI: 10.3389/fchem.2016.00015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/24/2016] [Indexed: 12/18/2022] Open
Abstract
Computational methods for Target Fishing (TF), also known as Target Prediction or Polypharmacology Prediction, can be used to discover new targets for small-molecule drugs. This may result in repositioning the drug in a new indication or improving our current understanding of its efficacy and side effects. While there is a substantial body of research on TF methods, there is still a need to improve their validation, which is often limited to a small part of the available targets and not easily interpretable by the user. Here we discuss how target-centric TF methods are inherently limited by the number of targets that can possibly predict (this number is by construction much larger in ligand-centric techniques). We also propose a new benchmark to validate TF methods, which is particularly suited to analyse how predictive performance varies with the query molecule. On average over approved drugs, we estimate that only five predicted targets will have to be tested to find two true targets with submicromolar potency (a strong variability in performance is however observed). In addition, we find that an approved drug has currently an average of eight known targets, which reinforces the notion that polypharmacology is a common and strong event. Furthermore, with the assistance of a control group of randomly-selected molecules, we show that the targets of approved drugs are generally harder to predict. The benchmark and a simple target prediction method to use as a performance baseline are available at http://ballester.marseille.inserm.fr/TF-benchmark.tar.gz.
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Affiliation(s)
- Antonio Peón
- Cancer Research Center of Marseille (Institut National de la Santé et de la Recherche Médicale U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Centre National de la Recherche Scientifique UMR7258) Marseille, France
| | - Cuong C Dang
- Cancer Research Center of Marseille (Institut National de la Santé et de la Recherche Médicale U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Centre National de la Recherche Scientifique UMR7258) Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille (Institut National de la Santé et de la Recherche Médicale U1068, Institut Paoli-Calmettes, Aix-Marseille Université, Centre National de la Recherche Scientifique UMR7258) Marseille, France
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Activity and property landscape modeling is at the interface of chemoinformatics and medicinal chemistry. Future Med Chem 2016; 7:1197-211. [PMID: 26132526 DOI: 10.4155/fmc.15.51] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Property landscape modeling (PLM) methods are at the interface of experimental sciences and computational chemistry. PLM are becoming a common strategy to describe systematically structure-property relationships of datasets. Thus far, PLM have been used mainly in medicinal chemistry and drug discovery. Herein, we survey advances on key topics on PLM with emphasis on questions often raised regarding the outcomes of the property landscape studies. We also emphasize on concepts of PLM that are being extended to other experimental areas beyond drug discovery. Topics discussed in this paper include applications of PLM to further characterize protein-ligand interactions, the utility of PLM as a quantitative and descriptive approach, and the statistical validation of property cliffs.
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Carrió P, Sanz F, Pastor M. Toward a unifying strategy for the structure-based prediction of toxicological endpoints. Arch Toxicol 2015; 90:2445-60. [PMID: 26553148 DOI: 10.1007/s00204-015-1618-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/19/2015] [Indexed: 01/13/2023]
Abstract
Most computational methods used for the prediction of toxicity endpoints are based on the assumption that similar compounds have similar biological properties. This principle can be exploited using computational methods like read across or quantitative structure-activity relationships. However, there is no general agreement about which method is the most appropriate for quantifying compound similarity neither for exploiting the similarity principle in order to obtain reliable estimations of the compound properties. Moreover, optimal similarity metrics and modeling methods might depend on the characteristics of the endpoints and training series used in each case. This study describes a comparative analysis of the predictive performance of diverse similarity metrics and modeling methods in toxicological applications. A collection of two quantitative (n = 660, n = 1114) and three qualitative (n = 447, n = 905, n = 1220) datasets representing very different endpoints of interest in drug safety evaluation and rigorous methods were used to estimate the external predictive ability in each case. The results confirm that no single approach produces the best results in all instances, and the best predictions were obtained using different tools in different situations. The trends observed in this study were exploited to propose a unifying strategy allowing the use of the most suitable method for every compound. A comparison of the quality of the predictions obtained by the unifying strategy with those obtained by standard prediction methods confirmed the usefulness of the proposed approach.
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Affiliation(s)
- Pau Carrió
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Carrer Dr. Aiguader 88, 08003, Barcelona, Spain.
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Feng Y, LoGrasso PV, Defert O, Li R. Rho Kinase (ROCK) Inhibitors and Their Therapeutic Potential. J Med Chem 2015; 59:2269-300. [PMID: 26486225 DOI: 10.1021/acs.jmedchem.5b00683] [Citation(s) in RCA: 244] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Rho kinases (ROCKs) belong to the serine-threonine family, the inhibition of which affects the function of many downstream substrates. As such, ROCK inhibitors have potential therapeutic applicability in a wide variety of pathological conditions including asthma, cancer, erectile dysfunction, glaucoma, insulin resistance, kidney failure, neuronal degeneration, and osteoporosis. To date, two ROCK inhibitors have been approved for clinical use in Japan (fasudil and ripasudil) and one in China (fasudil). In 1995 fasudil was approved for the treatment of cerebral vasospasm, and more recently, ripasudil was approved for the treatment of glaucoma in 2014. In this Perspective, we present a comprehensive review of the physiological and biological functions for ROCK, the properties and development of over 170 ROCK inhibitors as well as their therapeutic potential, the current status, and future considerations.
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Affiliation(s)
| | | | - Olivier Defert
- Amakem Therapeutics , Agoralaan A bis, 3590 Diepenbeek, Belgium
| | - Rongshi Li
- Center for Drug Discovery and Department of Pharmaceutical Sciences, College of Pharmacy, Cancer Genes and Molecular Regulation Program, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , 986805 Nebraska Medical Center, Omaha, Nebraska 68198, United States
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Naveja JJ, Medina-Franco JL. Activity landscape of DNA methyltransferase inhibitors bridges chemoinformatics with epigenetic drug discovery. Expert Opin Drug Discov 2015; 10:1059-70. [DOI: 10.1517/17460441.2015.1073257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Husby J, Bottegoni G, Kufareva I, Abagyan R, Cavalli A. Structure-based predictions of activity cliffs. J Chem Inf Model 2015; 55:1062-76. [PMID: 25918827 DOI: 10.1021/ci500742b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
In drug discovery, it is generally accepted that neighboring molecules in a given descriptor's space display similar activities. However, even in regions that provide strong predictability, structurally similar molecules can occasionally display large differences in potency. In QSAR jargon, these discontinuities in the activity landscape are known as "activity cliffs". In this study, we assessed the reliability of ligand docking and virtual ligand screening schemes in predicting activity cliffs. We performed our calculations on a diverse, independently collected database of cliff-forming cocrystals. Starting from ideal situations, which allowed us to establish our baseline, we progressively moved toward simulating more realistic scenarios. Ensemble- and template-docking achieved a significant level of accuracy, suggesting that, despite the well-known limitations of empirical scoring schemes, activity cliffs can be accurately predicted by advanced structure-based methods.
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Affiliation(s)
- Jarmila Husby
- †Department of Drug Discovery and Development-Computation, IIT-Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Giovanni Bottegoni
- †Department of Drug Discovery and Development-Computation, IIT-Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Irina Kufareva
- ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California 92161, United States
| | - Ruben Abagyan
- ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California 92161, United States
| | - Andrea Cavalli
- †Department of Drug Discovery and Development-Computation, IIT-Istituto Italiano di Tecnologia, 16163 Genova, Italy.,§Department of Pharmacy and Biotechnology, Università di Bologna, 40126 Bologna, Italy
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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Méndez-Lucio O, Kooistra AJ, Graaf CD, Bender A, Medina-Franco JL. Analyzing Multitarget Activity Landscapes Using Protein–Ligand Interaction Fingerprints: Interaction Cliffs. J Chem Inf Model 2015; 55:251-62. [DOI: 10.1021/ci500721x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Oscar Méndez-Lucio
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Albert J. Kooistra
- Division
of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Division
of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for
Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - José L. Medina-Franco
- Facultad
de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
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Abstract
Background Sound statistical validation is important to evaluate and compare the overall performance of (Q)SAR models. However, classical validation does not support the user in better understanding the properties of the model or the underlying data. Even though, a number of visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allow the investigation of model validation results are still lacking. Results We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. The approach applies the 3D viewer CheS-Mapper, an open-source application for the exploration of small molecules in virtual 3D space. The present work describes the new functionalities in CheS-Mapper 2.0, that facilitate the analysis of (Q)SAR information and allows the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. The approach is generic: It is model-independent and can handle physico-chemical and structural input features as well as quantitative and qualitative endpoints. Conclusions Visual validation with CheS-Mapper enables analyzing (Q)SAR information in the data and indicates how this information is employed by the (Q)SAR model. It reveals, if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org. Graphical abstract Comparing actual and predicted activity values with CheS-Mapper.
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Kupcewicz B, Jarzęcki AA, Małecka M, Krajewska U, Rozalski M. Cytotoxic activity of substituted chalcones in terms of molecular electronic properties. Bioorg Med Chem Lett 2014; 24:4260-5. [DOI: 10.1016/j.bmcl.2014.07.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/10/2014] [Accepted: 07/10/2014] [Indexed: 11/16/2022]
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Kuyoc-Carrillo VF, Medina-Franco JL. Progress in the Analysis of Multiple Activity Profile of Screening Data Using Computational Approaches. Drug Dev Res 2014; 75:313-23. [DOI: 10.1002/ddr.21209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Cruz-Monteagudo M, Medina-Franco JL, Pérez-Castillo Y, Nicolotti O, Cordeiro MND, Borges F. Activity cliffs in drug discovery: Dr Jekyll or Mr Hyde? Drug Discov Today 2014; 19:1069-80. [DOI: 10.1016/j.drudis.2014.02.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/23/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
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Willett P. The Calculation of Molecular Structural Similarity: Principles and Practice. Mol Inform 2014; 33:403-13. [DOI: 10.1002/minf.201400024] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/14/2014] [Indexed: 01/28/2023]
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41
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Rojas-Aguirre Y, Medina-Franco JL. Analysis of structure-Caco-2 permeability relationships using a property landscape approach. Mol Divers 2014; 18:599-610. [DOI: 10.1007/s11030-014-9514-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/28/2014] [Indexed: 12/14/2022]
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Guha R, Medina-Franco JL. On the validity versus utility of activity landscapes: are all activity cliffs statistically significant? J Cheminform 2014; 6:11. [PMID: 24694189 PMCID: PMC4021161 DOI: 10.1186/1758-2946-6-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 03/25/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Most work on the topic of activity landscapes has focused on their quantitative description and visual representation, with the aim of aiding navigation of SAR. Recent developments have addressed applications such as quantifying the proportion of activity cliffs, investigating the predictive abilities of activity landscape methods and so on. However, all these publications have worked under the assumption that the activity landscape models are "real" (i.e., statistically significant). RESULTS The current study addresses for the first time, in a quantitative manner, the significance of a landscape or individual cliffs in the landscape. In particular, we question whether the activity landscape derived from observed (experimental) activity data is different from a randomly generated landscape. To address this we used the SALI measure with six different data sets tested against one or more molecular targets. We also assessed the significance of the landscapes for single and multiple representations. CONCLUSIONS We find that non-random landscapes are data set and molecular representation dependent. For the data sets and representations used in this work, our results suggest that not all representations lead to non-random landscapes. This indicates that not all molecular representations should be used to a) interpret the SAR and b) combined to generate consensus models. Our results suggest that significance testing of activity landscape models and in particular, activity cliffs, is key, prior to the use of such models.
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Affiliation(s)
- Rajarshi Guha
- NIH Center for Advancing Translational Science, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - José L Medina-Franco
- Circuito Exterior, Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F. 04510, Mexico ; Current address: Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA
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Rationalization of activity cliffs of a sulfonamide inhibitor of DNA methyltransferases with induced-fit docking. Int J Mol Sci 2014; 15:3253-61. [PMID: 24566147 PMCID: PMC3958909 DOI: 10.3390/ijms15023253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/04/2022] Open
Abstract
Inhibitors of human DNA methyltransferases (DNMT) are of increasing interest to develop novel epi-drugs for the treatment of cancer and other diseases. As the number of compounds with reported DNMT inhibition is increasing, molecular docking is shedding light to elucidate their mechanism of action and further interpret structure–activity relationships. Herein, we present a structure-based rationalization of the activity of SW155246, a distinct sulfonamide compound recently reported as an inhibitor of human DNMT1 obtained from high-throughput screening. We used flexible and induce-fit docking to develop a binding model of SW155246 with a crystallographic structure of human DNMT1. Results were in excellent agreement with experimental information providing a three-dimensional structural interpretation of ‘activity cliffs’, e.g., analogues of SW155246 with a high structural similarity to the sulfonamide compound, but with no activity in the enzymatic assay.
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Medina-Franco JL, Méndez-Lucio O, Martinez-Mayorga K. The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:1-37. [DOI: 10.1016/bs.apcsb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chemoinformatic characterization of activity and selectivity switches of antiprotozoal compounds. Future Med Chem 2013; 6:281-94. [PMID: 24279680 DOI: 10.4155/fmc.13.173] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Benzimidazole derivatives are promising compounds for the treatment of parasitic infections. The structure-activity relationships of 91 benzimidazoles with activity against Trichomonas vaginalis and Giardia intestinalis were analyzed using a novel activity landscape modeling approach. RESULTS We identified two prominent cases of 'activity switches' and 'selectivity switches' where two R group substitutions in the benzimidazole scaffold completely invert the activity and selectivity pattern for T. vaginalis and G. intestinalis. CONCLUSION A chemoinformatic methodology was used to rapidly identify discrete structural changes around the central scaffold that are associated with large changes in biological activity for each parasite. The structure-activity relationships for the benzimidazole derivatives is smooth for both protozoan with few but markedly important activity cliffs.
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Medina-Franco JL, Edwards BS, Pinilla C, Appel JR, Giulianotti MA, Santos RG, Yongye AB, Sklar LA, Houghten RA. Rapid scanning structure-activity relationships in combinatorial data sets: identification of activity switches. J Chem Inf Model 2013; 53:1475-85. [PMID: 23705689 DOI: 10.1021/ci400192y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We present a general approach to describe the structure-activity relationships (SAR) of combinatorial data sets with activity for two biological endpoints with emphasis on the rapid identification of substitutions that have a large impact on activity and selectivity. The approach uses dual-activity difference (DAD) maps that represent a visual and quantitative analysis of all pairwise comparisons of one, two, or more substitutions around a molecular template. Scanning the SAR of data sets using DAD maps allows the visual and quantitative identification of activity switches defined as specific substitutions that have an opposite effect on the activity of the compounds against two targets. The approach also rapidly identifies single- and double-target R-cliffs, i.e., compounds where a single or double substitution around the central scaffold dramatically modifies the activity for one or two targets, respectively. The approach introduced in this report can be applied to any analogue series with two biological activity endpoints. To illustrate the approach, we discuss the SAR of 106 pyrrolidine bis-diketopiperazines tested against two formylpeptide receptors obtained from positional scanning deconvolution methods of mixture-based libraries.
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Affiliation(s)
- José L Medina-Franco
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida 34987, USA.
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