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Haridas PC, Ravichandran R, Shaikh N, Kishore P, Kumar Panda S, Banerjee K, Sekhar Chatterjee N. Authentication of the species identity of squid rings using UHPLC-Q-Orbitrap MS/MS-based lipidome fingerprinting and chemoinformatics. Food Chem 2024; 442:138525. [PMID: 38271906 DOI: 10.1016/j.foodchem.2024.138525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/20/2023] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Species mislabeling of commercial loliginidae squid can undermine important conservation efforts and prevent consumers from making informed decisions. A comprehensive lipidomic fingerprint of Uroteuthis singhalensis, Uroteuthis edulis, and Uroteuthis duvauceli rings was established using high-resolution mass spectrometry-based lipidomics and chemoinformatics analysis. The principal component analysis showed a clear separation of sample groups, with R2X and Q2 values of 0.97 and 0.85 for ESI+ and 0.96 and 0.86 for ESI-, indicating a good model fit. The optimized OPLS-DA and PLS-DA models could discriminate the species identity of validation samples with 100 % accuracy. A total of 67 and 90 lipid molecules were putatively identified as biomarkers in ESI+ and ESI-, respectively. Identified lipids, including PC(40:6), C14 sphingomyelin, PS(O-36:0), and PE(41:4), played an important role in species discrimination. For the first time, this study provides a detailed lipidomics profile of commercially important loliginidae squid and establishes a faster workflow for species authentication.
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Affiliation(s)
- Pranamya C Haridas
- National Reference Laboratory, ICAR-Central Institute of Fisheries Technology, Matsyapuri P.O., W. Island, Cochin 682029, India; Department of Chemical Oceanography, School of Marine Sciences, Cochin University of Science and Technology, Cochin 682016, India
| | - Rajesh Ravichandran
- National Reference Laboratory, ICAR-Central Institute of Fisheries Technology, Matsyapuri P.O., W. Island, Cochin 682029, India
| | - Nasiruddin Shaikh
- National Referral Laboratory, ICAR-National Research Centre for Grapes, Manjri Farm, Pune 412307, India
| | - Pankaj Kishore
- National Reference Laboratory, ICAR-Central Institute of Fisheries Technology, Matsyapuri P.O., W. Island, Cochin 682029, India
| | - Satyen Kumar Panda
- National Reference Laboratory, ICAR-Central Institute of Fisheries Technology, Matsyapuri P.O., W. Island, Cochin 682029, India; Food Safety and Standards Authority of India, FDA Bhawan, Kotla Road, New Delhi 110002, India
| | - Kaushik Banerjee
- National Referral Laboratory, ICAR-National Research Centre for Grapes, Manjri Farm, Pune 412307, India
| | - Niladri Sekhar Chatterjee
- National Reference Laboratory, ICAR-Central Institute of Fisheries Technology, Matsyapuri P.O., W. Island, Cochin 682029, India.
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2
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Merz KM, Wei GW, Zhu F. Editorial: Machine Learning in Bio- cheminformatics. J Chem Inf Model 2024; 64:2125-2128. [PMID: 38587006 DOI: 10.1021/acs.jcim.4c00444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Affiliation(s)
- Kenneth M Merz
- Department of Chemistry, Michigan State University, Lansing 48824, Michigan, United States
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, Lansing 48824, Michigan, United States
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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3
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Le Roch M, Renault J, Argouarch G, Lenci E, Trabocchi A, Roisnel T, Gouault N, Lalli C. Synthesis and Chemoinformatic Analysis of Fluorinated Piperidines as 3D Fragments for Fragment-Based Drug Discovery. J Org Chem 2024; 89:4932-4946. [PMID: 38451837 DOI: 10.1021/acs.joc.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The concise synthesis of a small library of fluorinated piperidines from readily available dihydropyridinone derivatives has been described. The effect of the fluorination on different positions has then been evaluated by chemoinformatic tools. In particular, the compounds' pKa's have been calculated, revealing that the fluorine atoms notably lowered their basicity, which is correlated to the affinity for hERG channels resulting in cardiac toxicity. The "lead-likeness" and three-dimensionality have also been evaluated to assess their ability as useful fragments for drug design. A random screening on a panel of representative proteolytic enzymes was then carried out and revealed that one scaffold is recognized by the catalytic pocket of 3CLPro (main protease of SARS-CoV-2 coronavirus).
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Affiliation(s)
- Myriam Le Roch
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
| | | | | | - Elena Lenci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Andrea Trabocchi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, Sesto Fiorentino, Florence 50019, Italy
| | - Thierry Roisnel
- Univ Rennes, Centre de Diffractométrie X (CDIFX), ISCR-UMR 6226, Rennes F-35000, France
| | | | - Claudia Lalli
- Univ Rennes, CNRS, ISCR-UMR 6226, Rennes F-35000, France
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4
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Vogt M. Chemoinformatic approaches for navigating large chemical spaces. Expert Opin Drug Discov 2024; 19:403-414. [PMID: 38300511 DOI: 10.1080/17460441.2024.2313475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Large chemical spaces (CSs) include traditional large compound collections, combinatorial libraries covering billions to trillions of molecules, DNA-encoded chemical libraries comprising complete combinatorial CSs in a single mixture, and virtual CSs explored by generative models. The diverse nature of these types of CSs require different chemoinformatic approaches for navigation. AREAS COVERED An overview of different types of large CSs is provided. Molecular representations and similarity metrics suitable for large CS exploration are discussed. A summary of navigation of CSs in generative models is provided. Methods for characterizing and comparing CSs are discussed. EXPERT OPINION The size of large CSs might restrict navigation to specialized algorithms and limit it to considering neighborhoods of structurally similar molecules. Efficient navigation of large CSs not only requires methods that scale with size but also requires smart approaches that focus on better but not necessarily larger molecule selections. Deep generative models aim to provide such approaches by implicitly learning features relevant for targeted biological properties. It is unclear whether these models can fulfill this ideal as validation is difficult as long as the covered CSs remain mainly virtual without experimental verification.
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Affiliation(s)
- Martin Vogt
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
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5
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Dolciami D, Ziolek RM, Davies DW, Carter M, Mok NY, Sherhod R. Exploiting Vector Pattern Diversity of Molecular Scaffolds for Cheminformatics Tasks in Drug Discovery. J Chem Inf Model 2024; 64:1966-1974. [PMID: 38437714 DOI: 10.1021/acs.jcim.3c01674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Chemical diversity is challenging to describe objectively. Despite this, various notions of chemical diversity are used throughout the medicinal chemistry optimization process in drug discovery. In this work, we show the usefulness of considering exploited vectors during different phases of the drug design process to provide a quantitative and objective description of chemical diversity. We have developed a concise and fast approach to enumerate and analyze the exploited vector patterns (EVPs) of molecular compound series, which can then be used in archetypal compound selection tasks, from hit matter identification to hit expansion and lead optimization. We first show that EVPs can be used to assess the progressibility of compounds in a fragment library design exercise. By considering EVPs, we then show how a set of compounds can be prioritized for hit expansion using EVP-based, customizable diversity sampling approaches, reducing the time taken and mitigating human biases. We also show that EVPs are a useful tool to analyze SAR data, offering the chance to uncover correlations between different vectors without predetermining the molecular scaffold structures. The codes used to perform these tasks are presented as easy-to-use Jupyter notebooks, which can be readily adapted for further related tasks.
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Affiliation(s)
| | | | | | | | - N Yi Mok
- BenevolentAI, 4-8 Maple Street, London W1T 5HD, U.K
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6
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Tripathi T, Singh DB, Tripathi T. Computational resources and chemoinformatics for translational health research. Adv Protein Chem Struct Biol 2024; 139:27-55. [PMID: 38448138 DOI: 10.1016/bs.apcsb.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The integration of computational resources and chemoinformatics has revolutionized translational health research. It has offered a powerful set of tools for accelerating drug discovery. This chapter overviews the computational resources and chemoinformatics methods used in translational health research. The resources and methods can be used to analyze large datasets, identify potential drug candidates, predict drug-target interactions, and optimize treatment regimens. These resources have the potential to transform the drug discovery process and foster personalized medicine research. We discuss insights into their various applications in translational health and emphasize the need for addressing challenges, promoting collaboration, and advancing the field to fully realize the potential of these tools in transforming healthcare.
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Affiliation(s)
- Tripti Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong, India
| | - Dev Bukhsh Singh
- Department of Biotechnology, Siddharth University, Kapilvastu, Siddharth Nagar, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Zoology, North-Eastern Hill University, Shillong, India.
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Tiwari SP, Shi W, Budhathoki S, Baker J, Sekizkardes AK, Zhu L, Kusuma VA, Hopkinson DP, Steckel JA. Creation of Polymer Datasets with Targeted Backbones for Screening of High-Performance Membranes for Gas Separation. J Chem Inf Model 2024; 64:638-652. [PMID: 38294781 DOI: 10.1021/acs.jcim.3c01232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
A simple approach was developed to computationally construct a polymer dataset by combining simplified molecular-input line-entry system (SMILES) strings of a targeted polymer backbone and a variety of molecular fragments. This method was used to create 14 polymer datasets by combining seven polymer backbones and molecules from two large molecular datasets (MOSES and QM9). Polymer backbones that were studied include four polydimethylsiloxane (PDMS) based backbones, poly(ethylene oxide) (PEO), poly(allyl glycidyl ether) (PAGE), and polyphosphazene (PPZ). The generated polymer datasets can be used for various cheminformatics tasks, including high-throughput screening for gas permeability and selectivity. This study utilized machine learning (ML) models to screen the polymers for CO2/CH4 and CO2/N2 gas separation using membranes. Several polymers of interest were identified. The results highlight that employing an ML model fitted to polymer selectivities leads to higher accuracy in predicting polymer selectivity compared to using the ratio of predicted permeabilities.
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Affiliation(s)
- Surya Prakash Tiwari
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Wei Shi
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Samir Budhathoki
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - James Baker
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Ali K Sekizkardes
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Lingxiang Zhu
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Victor A Kusuma
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
- NETL Support Contractor, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - David P Hopkinson
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
| | - Janice A Steckel
- National Energy Technology Laboratory, 626 Cochran Mill Road, Pittsburgh, Pennsylvania 15236, United States
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Tandi M, Tripathi N, Gaur A, Gopal B, Sundriyal S. Curation and cheminformatics analysis of a Ugi-reaction derived library (URDL) of synthetically tractable small molecules for virtual screening application. Mol Divers 2024; 28:37-50. [PMID: 36574164 DOI: 10.1007/s11030-022-10588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022]
Abstract
Virtual screening (VS) is an important approach in drug discovery and relies on the availability of a virtual library of synthetically tractable molecules. Ugi reaction (UR) represents an important multi-component reaction (MCR) that reliably produces a peptidomimetic scaffold. Recent literature shows that a tactically assembled Ugi adduct can be subjected to further chemical modifications to yield a variety of rings and scaffolds, thus, renewing the interest in this old reaction. Given the reliability and efficiency of UR, we collated an UR derived library (URDL) of small molecules (total = 5773) for VS. The synthesis of the majority of URDL molecules may be carried out in 1-2 pots in a time and cost-effective manner. The detailed analysis of the average property and chemical space of URDL was also carried out using the open-source Datawarrior program. The comparison with FDA-approved oral drugs and inhibitors of protein-protein interactions (iPPIs) suggests URDL molecules are 'clean', drug-like, and conform to a structurally distinct space from the other two categories. The average physicochemical properties of compounds in the URDL library lie closer to iPPI molecules than oral drugs thus suggesting that the URDL resource can be applied to discover novel iPPI molecules. The URDL molecules consist of diverse ring systems, many of which have not been exploited yet for drug design. Thus, URDL represents a small virtual library of drug-like molecules with unexplored chemical space designed for VS. The structures of all molecules of URDL, oral drugs, and iPPI compounds are being made freely accessible as supplementary information for broader application.
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Affiliation(s)
- Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Nancy Tripathi
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | - Animesh Gaur
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India
| | | | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Rajasthan, 333031, India.
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9
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Voinarovska V, Kabeshov M, Dudenko D, Genheden S, Tetko IV. When Yield Prediction Does Not Yield Prediction: An Overview of the Current Challenges. J Chem Inf Model 2024; 64:42-56. [PMID: 38116926 PMCID: PMC10778086 DOI: 10.1021/acs.jcim.3c01524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023]
Abstract
Machine Learning (ML) techniques face significant challenges when predicting advanced chemical properties, such as yield, feasibility of chemical synthesis, and optimal reaction conditions. These challenges stem from the high-dimensional nature of the prediction task and the myriad essential variables involved, ranging from reactants and reagents to catalysts, temperature, and purification processes. Successfully developing a reliable predictive model not only holds the potential for optimizing high-throughput experiments but can also elevate existing retrosynthetic predictive approaches and bolster a plethora of applications within the field. In this review, we systematically evaluate the efficacy of current ML methodologies in chemoinformatics, shedding light on their milestones and inherent limitations. Additionally, a detailed examination of a representative case study provides insights into the prevailing issues related to data availability and transferability in the discipline.
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Affiliation(s)
- Varvara Voinarovska
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
- TUM
Graduate School, Faculty of Chemistry, Technical
University of Munich, 85748 Garching, Germany
| | - Mikhail Kabeshov
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Dmytro Dudenko
- Enamine
Ltd., 78 Chervonotkatska str., 02094 Kyiv, Ukraine
| | - Samuel Genheden
- Molecular
AI, Discovery Sciences R&D, AstraZeneca, 431 83 Gothenburg, Sweden
| | - Igor V. Tetko
- Molecular
Targets and Therapeutics Center, Helmholtz Munich − Deutsches
Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Structural Biology, 85764 Neuherberg, Germany
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10
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Murali A, Panwar U, Singh SK. Exploring the Role of Chemoinformatics in Accelerating Drug Discovery: A Computational Approach. Methods Mol Biol 2024; 2714:203-213. [PMID: 37676601 DOI: 10.1007/978-1-0716-3441-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Cheminformatics and its role in drug discovery is expected to be the privileged approach in handling large number of chemical datasets. This approach contributes toward the pharmaceutical development and assessment of chemical compounds at a faster rate efficiently. Additionally, as technological advancement impacts research, cheminformatics is being used more and more in the field of health science. This chapter describes the concepts of cheminformatics along with its involvement in drug discovery with a case study.
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Affiliation(s)
- Aarthy Murali
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Department of Data Sciences, Centre of Biomedical Research, SGPGIMS Campus, Lucknow, Uttar Pradesh, India
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11
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Aires-de-Sousa J. GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit. Mol Inform 2024; 43:e202300190. [PMID: 37885368 DOI: 10.1002/minf.202300190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
GUIDEMOL is a Python computer program based on the RDKit software to process molecular structures and calculate molecular descriptors with a graphical user interface using the tkinter package. It can calculate descriptors already implemented in RDKit as well as grid representations of 3D molecular structures using the electrostatic potential or voxels. The GUIDEMOL app provides easy access to RDKit tools for chemoinformatics users with no programming skills and can be adapted to calculate other descriptors or to trigger other procedures. A command line interface (CLI) is also provided for the calculation of grid representations. The source code is available at https://github.com/jairesdesousa/guidemol.
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Affiliation(s)
- Joao Aires-de-Sousa
- LAQV and REQUIMTE, Chemistry Department, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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12
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Aribisala JO, Sabiu S. Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy. J Biomol Struct Dyn 2024; 42:298-313. [PMID: 36974951 DOI: 10.1080/07391102.2023.2192808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023]
Abstract
Antibacterial resistance to β-lactams in microorganisms has been attributed majorly to alterations in penicillin-binding proteins (PBPs) coupled with β-lactams' inactivation by β-lactamase. Consequently, the identification of a novel class of therapeutics with improved modulatory action on the PBPs is imperative and plant secondary metabolites, including phenolics, have found relevance in this regard. For the first time in this study, the over 10,000 phenolics currently known were computationally evaluated against PBP3 of Pseudomonas aeruginosa, a superbug implicated in several nosocomial infections. In doing this, a library of phenolics with an affinity for PBP3 of P. aeruginosa was screened using structure-activity relationship-based pharmacophore and molecular docking approaches. Subsequent thermodynamic screening of the top five phenolics with higher docking scores, more drug-likeness attributes, and feasible synthetic accessibility was achieved through a 120 ns molecular dynamic (MD) simulation. Four of the top five hits had higher binding free energy than cefotaxime (-18.72 kcal/mol), with catechin-3-rhamside having the highest affinity (-28.99 kcal/mol). All the hits were stable at the active site of the PBP3, with catechin-3-rhamside being the most stable (2.14 Å), and established important interactions with Ser294, implicated in the catalytic activity of PBP3. Also, PBP3 became more compact with less fluctuation of the active site amino acid residues following the binding of the hits. These observations are indicative of the potential of the test compounds as PBP3 inhibitors, with catechin-3-rhamside being the most prominent of the compounds that could be further improved for enhanced druggability against PBP3 in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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13
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Liu Y, Cao Y. Protein-Ligand Blind Docking Using CB-Dock2. Methods Mol Biol 2024; 2714:113-125. [PMID: 37676595 DOI: 10.1007/978-1-0716-3441-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Protein-ligand blind docking is a widely used method for studying the binding sites and poses of ligands and receptors in pharmaceutical and biological research. Recently, our new blind docking server named CB-Dock2 has been released and is currently being utilized by researchers worldwide. CB-Dock2 outperforms state-of-the-art methods due to its accuracy in binding site identification and binding pose prediction, which are enabled by its knowledge-based docking engine. This highly automated server offers interactive and intuitive input and output web interfaces, making it an efficient and user-friendly tool for the bioinformatics and cheminformatics communities. This chapter provides a brief overview of the methods, followed by a detailed guide on using the CB-Dock2 server. Additionally, we present a case study that evaluates the performance of protein-ligand blind docking using this tool.
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Affiliation(s)
- Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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14
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Panek A, Wójcik P, Świzdor A, Szaleniec M, Janeczko T. Biotransformation of Δ 1-Progesterone Using Selected Entomopathogenic Filamentous Fungi and Prediction of Its Products' Bioactivity. Int J Mol Sci 2023; 25:508. [PMID: 38203679 PMCID: PMC10779271 DOI: 10.3390/ijms25010508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
This research aimed at obtaining new derivatives of pregn-1,4-diene-3,20-dione (Δ1-progesterone) (2) through microbiological transformation. For the role of catalysts, we used six strains of entomopathogenic filamentous fungi (Beauveria bassiana KCh J1.5, Beauveria caledonica KCh J3.3, Isaria fumosorosea KCh J2, Isaria farinosa KCh KW1.1, Isaria tenuipes MU35, and Metarhizium robertsii MU4). The substrate (2) was obtained by carrying out an enzymatic 1,2-dehydrogenation on an increased scale (3.5 g/L) using a recombinant cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans. All selected strains were characterized by the high biotransformation capacity for the used substrate. As a result of the biotransformation, six steroid derivatives were obtained: 11α-hydroxypregn-1,4-diene-3,20-dione (3), 6β,11α-dihydroxypregn-1,4-diene-3,20-dione (4), 6β-hydroxypregn-1,4-diene-3,11,20-trione (5), 6β,17α-dihydroxypregn-1,4-diene-3,20-dione (6), 6β,17β-dihydroxyandrost-1,4-diene-3-one (7), and 12β,17α-dihydroxypregn-1,4-diene-3,20-dione (8). The results show evident variability of the biotransformation process between strains of the tested biocatalysts from different species described as entomopathogenic filamentous fungi. The obtained products were tested in silico using cheminformatics tools for their pharmacokinetic and pharmacodynamic properties, proving their potentially high biological activities. This study showed that the obtained compounds may have applications as effective inhibitors of testosterone 17β-dehydrogenase. Most of the obtained products should, also with a high probability, find potential uses as androgen antagonists, a prostate as well as menopausal disorders treatment. They should also demonstrate immunosuppressive, erythropoiesis-stimulating, and anti-inflammatory properties.
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Affiliation(s)
- Anna Panek
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
| | - Patrycja Wójcik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (P.W.); (M.S.)
| | - Alina Świzdor
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
| | - Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland; (P.W.); (M.S.)
| | - Tomasz Janeczko
- Department of Food Chemistry and Biocatalysis, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland;
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15
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Fliszkiewicz B, Sajdak M. Fragments quantum descriptors in classification of bio-accumulative compounds. J Mol Graph Model 2023; 125:108584. [PMID: 37611341 DOI: 10.1016/j.jmgm.2023.108584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/25/2023]
Abstract
The aim of the following research is to assess the applicability of calculated quantum properties of molecular fragments as molecular descriptors in machine learning classification task. The research is based on bio-concentration and QM9-extended databases. A number of compounds with results from quantum-chemical calculations conducted with Psi4 quantum chemistry package was also added to the quantum properties database. Classification results are compared with a baseline of random guesses and predictions obtained with the traditional RDKit generated molecular descriptors. Chosen classification metrics show that results obtained with fragments quantum descriptors fall between results from baseline and those provided by molecular descriptors widely applied in cheminformatics. According to the results, the implementation of principal component analysis, causes a drop in categorization metrics.
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Affiliation(s)
- Bartłomiej Fliszkiewicz
- Department of New Technologies and Chemistry, Military University of Technology, Kaliskiego 2, Warsaw, 00-908, Poland.
| | - Marcin Sajdak
- Faculty of Energy and Environmental Engineering, Silesian University of Technology, Akademicka 2A, Gliwice, 44-109, Poland; School of Chemical Engineering, University of Birmingham, S W Campus, Birmingham, B15 TT, United Kingdom
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16
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Aiman S, Ahmad A, Khan A, Ali Y, Malik A, Alkholief M, Akhtar S, Khan RS, Li C, Jalil F, Ali Y. Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella Sonnei: Immunoinformatics and chemoinformatics approaches. PLoS One 2023; 18:e0289773. [PMID: 37992050 PMCID: PMC10664945 DOI: 10.1371/journal.pone.0289773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/25/2023] [Indexed: 11/24/2023] Open
Abstract
Shigella sonnei is a gram-negative bacterium and is the primary cause of shigellosis in advanced countries. An exceptional rise in the prevalence of the disease has been reported in Asia, the Middle East, and Latin America. To date, no preventive vaccine is available against S. sonnei infections. This pathogen has shown resistances towards both first- and second-line antibiotics. Therefore, an effective broad spectrum vaccine development against shigellosis is indispensable. In the present study, vaccinomics-aided immunoinformatics strategies were pursued to identify potential vaccine candidates from the S. sonnei whole proteome data. Pathogen essential proteins that are non-homologous to human and human gut microbiome proteome set, are feasible candidates for this purpose. Three antigenic outer membrane proteins were prioritized to predict lead epitopes based on reverse vaccinology approach. Multi-epitope-based chimeric vaccines was designed using lead B- and T-cell epitopes combined with suitable linker and adjuvant peptide sequences to enhance immune responses against the designed vaccine. The SS-MEVC construct was prioritized based on multiple physicochemical, immunological properties, and immune-receptors docking scores. Immune simulation analysis predicted strong immunogenic response capability of the designed vaccine construct. The Molecular dynamic simulations analysis ensured stable molecular interactions of lead vaccine construct with the host receptors. In silico restriction and cloning analysis predicted feasible cloning capability of the SS-MEVC construct within the E. coli expression system. The proposed vaccine construct is predicted to be more safe, effective and capable of inducing robust immune responses against S. sonnei infections and may be worthy of examination via in vitro/in vivo assays.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Islamabad, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Raham Sher Khan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Ali
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Hong Kong
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17
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Barrera-Vázquez OS, Montenegro-Herrera SA, Martínez-Enríquez ME, Escobar-Ramírez JL, Magos-Guerrero GA. Selection of Mexican Medicinal Plants by Identification of Potential Phytochemicals with Anti-Aging, Anti-Inflammatory, and Anti-Oxidant Properties through Network Analysis and Chemoinformatic Screening. Biomolecules 2023; 13:1673. [PMID: 38002355 PMCID: PMC10669844 DOI: 10.3390/biom13111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Many natural products have been acquired from plants for their helpful properties. Medicinal plants are used for treating a variety of pathologies or symptoms. The axes of many pathological processes are inflammation, oxidative stress, and senescence. This work is focused on identifying Mexican medicinal plants with potential anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence effects through network analysis and chemoinformatic screening of their phytochemicals. We used computational methods to analyze drug-like phytochemicals in Mexican medicinal plants, multi-target compounds, and signaling pathways related to anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence mechanisms. A total of 1373 phytochemicals are found in 1025 Mexican medicinal plants, and 148 compounds showed no harmful functionalities. These compounds displayed comparable structures with reference molecules. Based on their capacity to interact with pharmacological targets, three clusters of Mexican medicinal plants have been established. Curatella americana, Ximenia americana, Malvastrum coromandelianum, and Manilkara zapota all have anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence effects. Plumeria rubra, Lonchocarpus yucatanensis, and Salvia polystachya contained phytochemicals with anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence reported activity. Lonchocarpus guatemalensis, Vallesia glabra, Erythrina oaxacana, and Erythrina sousae have drug-like phytochemicals with potential anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence effects. Between the drug-like phytochemicals, lonchocarpin, vallesine, and erysotrine exhibit potential anti-oxidant, anti-inflammatory, anti-aging, and anti-senescence effects. For the first time, we conducted an initial virtual screening of selected Mexican medicinal plants, which was subsequently confirmed in vivo, evaluating the anti-inflammatory activity of Lonchocarpus guatemalensis Benth in mice.
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Affiliation(s)
- Oscar Salvador Barrera-Vázquez
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (O.S.B.-V.); (M.E.M.-E.); (J.L.E.-R.)
| | | | - María Elena Martínez-Enríquez
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (O.S.B.-V.); (M.E.M.-E.); (J.L.E.-R.)
| | - Juan Luis Escobar-Ramírez
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (O.S.B.-V.); (M.E.M.-E.); (J.L.E.-R.)
| | - Gil Alfonso Magos-Guerrero
- Department of Pharmacology, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 04510, Mexico; (O.S.B.-V.); (M.E.M.-E.); (J.L.E.-R.)
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18
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Liu X, Cheng Q, Sun D, Wei W, Zheng Z. Anonymous Pattern Molecular Fingerprint and its Applications on Property Identification. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:3759-3771. [PMID: 37812549 DOI: 10.1109/tcbb.2023.3322697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Molecular fingerprints are significant cheminformatics tools to map molecules into vectorial space according to their characteristics in diverse functional groups, atom sequences, and other topological structures. In this paper, we investigate a novel molecular fingerprint Anonymous-FP that possesses abundant perception about the underlying interactions shaped in small, medium, and large-scale atom chains. In detail, the possible atom chains from each molecule are sampled and extended as anonymous atom chains using an anonymous encoding manner. After that, the molecular fingerprint Anonymous-FP is embedded into vectorial space in virtue of the Natural Language Processing technique PV-DBOW. Anonymous-FP is studied on molecular property identification via molecule classification experiments on a series of molecule databases and has shown valuable advantages such as less dependence on prior knowledge, rich information content, full structural significance, and high experimental performance. During the experimental verification, the scale of the atom chain or its anonymous pattern is found significant to the overall representation ability of Anonymous-FP. Generally, the typical scale r = 8 could enhance the molecule classification performance, and specifically, Anonymous-FP gains the classification accuracy to above 93% on all NCI datasets.
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19
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Cho YR, Jo KA, Park SY, Choi JW, Kim G, Kim TY, Lee S, Lee DH, Kim SK, Lee D, Lee S, Lim S, Woo SO, Byun S, Kim JY. Combination of UHPLC-MS/MS with context-specific network and cheminformatic approaches for identifying bioactivities and active components of propolis. Food Res Int 2023; 172:113134. [PMID: 37689898 DOI: 10.1016/j.foodres.2023.113134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023]
Abstract
Discovering new bioactivities and identifying active compounds of food materials are major fields of study in food science. However, the process commonly requires extensive experiments and can be technically challenging. In the current study, we employed network biology and cheminformatic approaches to predict new target diseases, active components, and related molecular mechanisms of propolis. Applying UHPLC-MS/MS analysis results of propolis to Context-Oriented Directed Associations (CODA) and Combination-Oriented Natural Product Database with Unified Terminology (COCONUT) systems indicated atopic dermatitis as a novel target disease. Experimental validation using cell- and human tissue-based models confirmed the therapeutic potential of propolis against atopic dermatitis. Moreover, we were able to find the major contributing compounds as well as their combinatorial effects responsible for the bioactivity of propolis. The CODA/COCONUT system also provided compound-associated genes explaining the underlying molecular mechanism of propolis. These results highlight the potential use of big data-driven network biological approaches to aid in analyzing the impact of food constituents at a systematic level.
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Affiliation(s)
- Ye-Ryeong Cho
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Kyeong Ah Jo
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Soo-Yeon Park
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Jae-Won Choi
- Department of Physical Education, Yonsei University, Seoul 03722, Republic of Korea
| | - Gwangmin Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Tae Yeon Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Soohwan Lee
- Department of Food Science and Biotechnology, Gachon University, Gyeonggi 13120, Republic of Korea
| | - Doo-Hee Lee
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung-Kuk Kim
- Department of Agrobiology, Division of Apiculture, National Institute of Agricultural Sciences, Wanju 55365, Republic of Korea
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Seungki Lee
- National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Seokwon Lim
- Department of Food Science and Biotechnology, Gachon University, Gyeonggi 13120, Republic of Korea
| | - Soon Ok Woo
- Department of Agrobiology, Division of Apiculture, National Institute of Agricultural Sciences, Wanju 55365, Republic of Korea
| | - Sanguine Byun
- Department of Biotechnology, Yonsei University, Seoul 03722, Republic of Korea.
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea.
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20
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Muralitharan D, Varadharajan V, Venkidasamy B. Cheminformatics and systems pharmacology approaches to unveil the potential plant bioactives to combat COVID-19. J Mol Recognit 2023; 36:e3055. [PMID: 37658788 DOI: 10.1002/jmr.3055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
COVID-19 was a global pandemic in the year 2020. Several treatment options failed to cure the disease. Thus, plant-based medicines are becoming a trend nowadays due to their less side effects. Bioactive chemicals from natural sources have been utilised for centuries as treatment options for a variety of ailments. To find out the potent bioactive compounds to counteract COVID-19, we use systems pharmacology and cheminformatics. They use the definitive data and predict the possible outcomes. In this study, we collected a total of 72 phytocompounds from the medicinally important plants such as Garcinia mangostana and Cinnamomum verum, of which 13 potential phytocompounds were identified to be active against the COVID-19 infection based on Swiss Target Prediction and compound target network analysis. These phytocompounds were annotated to identify the specific human receptor that targets COVID-19-specific genes such as MAPK8, MAPK14, ACE, CYP3A4, TLR4 and TYK2. Among these, compounds such as smeathxanthone A, demethylcalabaxanthone, mangostanol, trapezifolixanthone from Garcinia mangostana and camphene from C. verum were putatively target various COVID-19-related genes. Molecular docking results showed that smeathxanthone A and demethylcalabaxanthone exhibit increased binding efficiency towards the COVID-19-related receptor proteins. These compounds also showed efficient putative pharmacoactive properties than the commercial drugs ((R)-remdesivir, favipiravir and hydroxychloroquine) used to cure COVID-19. In conclusion, our study highlights the use of cheminformatics approach to unravel the potent and novel phytocompounds against COVID-19. These phytocompounds may be safer to use, more efficient and less harmful. This study highlights the value of natural products in the search for new drugs and identifies candidates with great promise.
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Affiliation(s)
- Dhivyadharshini Muralitharan
- Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | | | - Baskar Venkidasamy
- Department of Oral & Maxillofacial Surgery, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
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21
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Matos GDR, Pak S, Rizzo RC. Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. J Chem Inf Model 2023; 63:5803-5822. [PMID: 37698425 PMCID: PMC10694857 DOI: 10.1021/acs.jcim.3c01031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Structure-based methods that employ principles of de novo design can be used to construct small organic molecules from scratch using pre-existing fragment libraries to sample chemical space and are an important class of computational algorithms for drug-lead discovery. Here, we present a powerful new design method for DOCK6 that employs a Descriptor-Driven De Novo strategy (termed D3N) in which user-defined cheminformatics descriptors (and their target ranges) are calculated at each layer of growth using the open-source toolkit RDKit. The objective is to tailor ligand growth toward desirable regions of chemical space. The approach was extensively validated through: (1) comparison of cheminformatics descriptors computed using the new DOCK6/RDKit interface versus the standard Python/RDKit installation, (2) examination of descriptor distributions generated using D3N growth under different conditions (target ranges and environments), and (3) construction of ligands with very tight (pinpoint) descriptor ranges using clinically relevant compounds as a reference. Our testing confirms that the new DOCK6/RDKit integration is robust, showcases how the new D3N routines can be used to direct sampling around user-defined chemical spaces, and highlights the utility of on-the-fly descriptor calculations for ligand design to important drug targets.
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Affiliation(s)
- Guilherme Duarte Ramos Matos
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Instituto de Química, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Steven Pak
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Robert C. Rizzo
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
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22
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Chen Y, Liu Y, Chen N, Jin Y, Yang R, Yao H, Kong DX. A chemoinformatic analysis on natural glycosides with respect to biological origin and structural class. Nat Prod Rep 2023; 40:1464-1478. [PMID: 37070562 DOI: 10.1039/d2np00089j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Covering: up to 202216.19% of reported natural products (NPs) in the Dictionary of Natural Products (DNP) are glycosides. As one of the most important NPs' structural modifications, glycosylation can change the NPs' polarity, making the aglycones more amphipathic. However, until now, little is known about the general distribution profile of the natural glycosides in different biological sources or structural types. The reason, structural or species preferences of the natural glycosylation remain unclear. In this highlight, chemoinformatic methods were employed to analyze the natural glycosides from DNP, the most comprehensively annotated NP database. We found that the glycosylation ratios of NPs from plants, bacteria, animals and fungi decrease successively, which are 24.99%, 20.84%, 8.40% and 4.48%, respectively. Echinoderm-derived NPs (56.11%) are the most frequently glycosylated, while those produced by molluscs (1.55%), vertebrates (2.19%) and Rhodophyta (3.00%) are the opposite. Among the diverse structural types, a large proportion of steroids (45.19%), tannins (44.78%) and flavonoids (39.21%) are glycosides, yet aminoacids and peptides (5.16%), alkaloids (5.66%) are comparatively less glycosylated. Even within the same biological source or structural type, their glycosylation rates fluctuate drastically between sub- or cross-categories. The substitute patterns of flavonoid and terpenoid glycosides and the most frequently glycosylated scaffolds were identified. NPs with different glycosylation levels occupy different chemical spaces of physicochemical property and scaffold. These findings could help us to interpret the preference of NPs' glycosylation and investigate how NP glycosylation could aid NP-based drug discovery.
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Affiliation(s)
- Yinliang Chen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - Yi Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - Nianhang Chen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - Yuting Jin
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - Ruofei Yang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - Hucheng Yao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China.
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23
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de Oliveira AA, Carmo Silva LD, Neves BJ, Fiaia Costa VA, Muratov EN, Andrade CH, de Almeida Soares CM, Alves VM, Pereira M. Cheminformatics-driven discovery of hit compounds against Paracoccidioides spp. Future Med Chem 2023; 15:1553-1567. [PMID: 37727967 DOI: 10.4155/fmc-2022-0288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
Aims: The development of safe and effective therapies for treating paracoccidioidomycosis using computational strategies were employed to discover anti-Paracoccidioides compounds. Materials & methods: We 1) collected, curated and integrated the largest library of compounds tested against Paracoccidioides spp.; 2) employed a similarity search to virtually screen the ChemBridge database and select nine compounds for experimental evaluation; 3) performed an experimental evaluation to determine the minimum inhibitory concentration and minimum fungicidal concentration as well as cytotoxicity; and 4) employed computational tools to identify potential targets for the most active compounds. Seven compounds presented activity against Paracoccidioides spp. Conclusion: These compounds are new hits with a predicted mechanisms of action, making them potentially attractive to develop new compounds.
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Affiliation(s)
- Amanda Alves de Oliveira
- Institute of Tropical Pathology & Public Health, Federal University of Goiás, Goiânia, 74690-900, Brazil
- Laboratory for Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, 74690-900, Brazil
| | - Lívia do Carmo Silva
- Laboratory for Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, 74690-900, Brazil
| | - Bruno Junior Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, 74690-900, Brazil
| | | | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology & Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599, USA
- Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, 58051-900, Brazil
| | - Carolina Horta Andrade
- Laboratory for Molecular Modeling & Design, Faculty of Pharmacy, Federal University of Goiás, 74690-900, Brazil
| | | | - Vinicius M Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology & Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC 27599, USA
- Laboratory for Molecular Modeling & Design, Faculty of Pharmacy, Federal University of Goiás, 74690-900, Brazil
| | - Maristela Pereira
- Laboratory for Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, 74690-900, Brazil
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24
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Lee BK, Mayhew EJ, Sanchez-Lengeling B, Wei JN, Qian WW, Little KA, Andres M, Nguyen BB, Moloy T, Yasonik J, Parker JK, Gerkin RC, Mainland JD, Wiltschko AB. A principal odor map unifies diverse tasks in olfactory perception. Science 2023; 381:999-1006. [PMID: 37651511 DOI: 10.1126/science.ade4401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Mapping molecular structure to odor perception is a key challenge in olfaction. We used graph neural networks to generate a principal odor map (POM) that preserves perceptual relationships and enables odor quality prediction for previously uncharacterized odorants. The model was as reliable as a human in describing odor quality: On a prospective validation set of 400 out-of-sample odorants, the model-generated odor profile more closely matched the trained panel mean than did the median panelist. By applying simple, interpretable, theoretically rooted transformations, the POM outperformed chemoinformatic models on several other odor prediction tasks, indicating that the POM successfully encoded a generalized map of structure-odor relationships. This approach broadly enables odor prediction and paves the way toward digitizing odors.
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Affiliation(s)
- Brian K Lee
- Google Research, Brain Team, Cambridge, MA, USA
| | - Emily J Mayhew
- Monell Chemical Senses Center, Philadelphia, PA, USA
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, MI, USA
| | | | | | - Wesley W Qian
- Google Research, Brain Team, Cambridge, MA, USA
- Osmo Labs, PBC, Cambridge, MA, USA
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | | | | | - Theresa Moloy
- Monell Chemical Senses Center, Philadelphia, PA, USA
| | - Jacob Yasonik
- Google Research, Brain Team, Cambridge, MA, USA
- Osmo Labs, PBC, Cambridge, MA, USA
| | - Jane K Parker
- Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, UK
| | - Richard C Gerkin
- Google Research, Brain Team, Cambridge, MA, USA
- Osmo Labs, PBC, Cambridge, MA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Joel D Mainland
- Monell Chemical Senses Center, Philadelphia, PA, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
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25
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Alsaady IM, Bajrai LH, Alandijany TA, Gattan HS, El-Daly MM, Altwaim SA, Alqawas RT, Dwivedi VD, Azhar EI. Cheminformatics Strategies Unlock Marburg Virus VP35 Inhibitors from Natural Compound Library. Viruses 2023; 15:1739. [PMID: 37632081 PMCID: PMC10459822 DOI: 10.3390/v15081739] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
The Ebola virus and its close relative, the Marburg virus, both belong to the family Filoviridae and are highly hazardous and contagious viruses. With a mortality rate ranging from 23% to 90%, depending on the specific outbreak, the development of effective antiviral interventions is crucial for reducing fatalities and mitigating the impact of Marburg virus outbreaks. In this investigation, a virtual screening approach was employed to evaluate 2042 natural compounds for their potential interactions with the VP35 protein of the Marburg virus. Average and worst binding energies were calculated for all 20 poses, and compounds that exhibited binding energies <-6 kcal/mol in both criteria were selected for further analysis. Based on binding energies, only six compounds (Estradiol benzoate, INVEGA (paliperidone), Isosilybin, Protopanaxadiol, Permethrin, and Bufalin) were selected for subsequent investigations, focusing on interaction analysis. Among these selected compounds, Estradiol benzoate, INVEGA (paliperidone), and Isosilybin showed strong hydrogen bonds, while the others did not. In this study, the compounds Myricetin, Isosilybin, and Estradiol benzoate were subjected to a molecular dynamics (MD) simulation and free binding energy calculation using MM/GBSA analysis. The reference component Myricetin served as a control. Estradiol benzoate exhibited the most stable and consistent root-mean-square deviation (RMSD) values, whereas Isosilybin showed significant fluctuations in RMSD. The compound Estradiol benzoate exhibited the lowest ΔG binding free energy (-22.89 kcal/mol), surpassing the control compound's binding energy (-9.29 kcal/mol). Overall, this investigation suggested that Estradiol benzoate possesses favorable binding free energies, indicating a potential inhibitory mechanism against the VP35 protein of the Marburg virus. The study proposes that these natural compounds could serve as a therapeutic option for preventing Marburg virus infection. However, experimental validation is required to further corroborate these findings.
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Affiliation(s)
- Isra M. Alsaady
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Hattan S. Gattan
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Sarah A. Altwaim
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rahaf T. Alqawas
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21362, Saudi Arabia;
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Tamil Nadu 602105, India
| | - Esam I. Azhar
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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Lanini J, Santarossa G, Sirockin F, Lewis R, Fechner N, Misztela H, Lewis S, Maziarz K, Stanley M, Segler M, Stiefl N, Schneider N. PREFER: A New Predictive Modeling Framework for Molecular Discovery. J Chem Inf Model 2023; 63:4497-4504. [PMID: 37487018 DOI: 10.1021/acs.jcim.3c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Machine-learning and deep-learning models have been extensively used in cheminformatics to predict molecular properties, to reduce the need for direct measurements, and to accelerate compound prioritization. However, different setups and frameworks and the large number of molecular representations make it difficult to properly evaluate, reproduce, and compare them. Here we present a new PREdictive modeling FramEwoRk for molecular discovery (PREFER), written in Python (version 3.7.7) and based on AutoSklearn (version 0.14.7), that allows comparison between different molecular representations and common machine-learning models. We provide an overview of the design of our framework and show exemplary use cases and results of several representation-model combinations on diverse data sets, both public and in-house. Finally, we discuss the use of PREFER on small data sets. The code of the framework is freely available on GitHub.
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Affiliation(s)
- Jessica Lanini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Gianluca Santarossa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Finton Sirockin
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Richard Lewis
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Nikolas Fechner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | | | - Sarah Lewis
- Microsoft Research AI4Science, Cambridge CB1 2FB, U.K
| | | | - Megan Stanley
- Microsoft Research AI4Science, Cambridge CB1 2FB, U.K
| | - Marwin Segler
- Microsoft Research AI4Science, Cambridge CB1 2FB, U.K
| | - Nikolaus Stiefl
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Nadine Schneider
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
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Lee ML, Farag S, Del Cid JS, Bashore C, Hallenbeck KK, Gobbi A, Cunningham CN. Identification of Macrocyclic Peptide Families from Combinatorial Libraries Containing Noncanonical Amino Acids Using Cheminformatics and Bioinformatics Inspired Clustering. ACS Chem Biol 2023; 18:1425-1434. [PMID: 37220419 PMCID: PMC10278063 DOI: 10.1021/acschembio.3c00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
In the past decade, macrocyclic peptides gained increasing interest as a new therapeutic modality to tackle intracellular and extracellular therapeutic targets that had been previously classified as "undruggable". Several technological advances have made discovering macrocyclic peptides against these targets possible: 1) the inclusion of noncanonical amino acids (NCAAs) into mRNA display, 2) increased availability of next generation sequencing (NGS), and 3) improvements in rapid peptide synthesis platforms. This type of directed-evolution based screening can produce large numbers of potential hit sequences given that DNA sequencing is the functional output of this platform. The current standard for selecting hit peptides from these selections for downstream follow-up relies on the frequency counting and sorting of unique peptide sequences which can result in the generation of false negatives due to technical reasons including low translation efficiency or other experimental factors. To overcome our inability to detect weakly enriched peptide sequences among our large data sets, we wanted to develop a clustering method that would enable the identification of peptide families. Unfortunately, utilizing traditional clustering algorithms, such as ClustalW, is not possible for this technology due to the incorporation of NCAAs in these libraries. Therefore, we developed a new atomistic clustering method with a Pairwise Aligned Peptide (PAP) chemical similarity metric to perform sequence alignments and identify macrocyclic peptide families. With this method, low enriched peptides, including isolated sequences (singletons), can now be clustered into families providing a comprehensive analysis of NGS data resulting from macrocycle discovery selections. Additionally, upon identification of a hit peptide with the desired activity, this clustering algorithm can be used to identify derivatives from the initial data set for structure-activity relationship (SAR) analysis without requiring additional selection experiments.
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Affiliation(s)
- Man-Ling Lee
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sherif Farag
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joselyn S. Del Cid
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Charlene Bashore
- Biological
Chemistry, Genentech Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Alberto Gobbi
- Discovery
Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Peptide
Therapeutics, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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28
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Broni E, Ashley C, Adams J, Manu H, Aikins E, Okom M, Miller WA, Wilson MD, Kwofie SK. Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors. Int J Mol Sci 2023; 24:ijms24076298. [PMID: 37047270 PMCID: PMC10094735 DOI: 10.3390/ijms24076298] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Joseph Adams
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - Hammond Manu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Ebenezer Aikins
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Mary Okom
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
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29
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Richard AM, Lougee R, Adams M, Hidle H, Yang C, Rathman J, Magdziarz T, Bienfait B, Williams AJ, Patlewicz G. A New CSRML Structure-Based Fingerprint Method for Profiling and Categorizing Per- and Polyfluoroalkyl Substances (PFAS). Chem Res Toxicol 2023; 36:508-534. [PMID: 36862450 PMCID: PMC10031568 DOI: 10.1021/acs.chemrestox.2c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The term PFAS encompasses diverse per- and polyfluorinated alkyl (and increasingly aromatic) chemicals spanning industrial processes, commercial uses, environmental occurrence, and potential concerns. With increased chemical curation, currently exceeding 14,000 structures in the PFASSTRUCTV5 inventory on EPA's CompTox Chemicals Dashboard, has come increased motivation to profile, categorize, and analyze the PFAS structure space using modern cheminformatics approaches. Making use of the publicly available ToxPrint chemotypes and ChemoTyper application, we have developed a new PFAS-specific fingerprint set consisting of 129 TxP_PFAS chemotypes coded in CSRML, a chemical-based XML-query language. These are split into two groups, the first containing 56 mostly bond-type ToxPrints modified to incorporate attachment to either a CF group or F atom to enforce proximity to the fluorinated portion of the chemical. This focus resulted in a dramatic reduction in TxP_PFAS chemotype counts relative to the corresponding ToxPrint counts (averaging 54%). The remaining TxP_PFAS chemotypes consist of various lengths and types of fluorinated chains, rings, and bonding patterns covering indications of branching, alternate halogenation, and fluorotelomers. Both groups of chemotypes are well represented across the PFASSTRUCT inventory. Using the ChemoTyper application, we show how the TxP_PFAS chemotypes can be visualized, filtered, and used to profile the PFASSTRUCT inventory, as well as to construct chemically intuitive, structure-based PFAS categories. Lastly, we used a selection of expert-based PFAS categories from the OECD Global PFAS list to evaluate a small set of analogous structure-based TxP_PFAS categories. TxP_PFAS chemotypes were able to recapitulate the expert-based PFAS category concepts based on clearly defined structure rules that can be computationally implemented and reproducibly applied to process large PFAS inventories without need to consult an expert. The TxP_PFAS chemotypes have the potential to support computational modeling, harmonize PFAS structure-based categories, facilitate communication, and allow for more efficient and chemically informed exploration of PFAS chemicals moving forward.
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Affiliation(s)
- Ann M Richard
- Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Ryan Lougee
- Oak Ridge Affiliated Universities Student Contractor to Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Matthew Adams
- Oak Ridge Affiliated Universities Student Contractor to Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Hannah Hidle
- Oak Ridge Affiliated Universities Student Contractor to Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Chihae Yang
- MN-AM, Molecular Networks GmbH & Altamira LLC, Nuremberg 90411, Germany
| | - James Rathman
- MN-AM, Molecular Networks GmbH & Altamira LLC, Nuremberg 90411, Germany
| | - Tomasz Magdziarz
- MN-AM, Molecular Networks GmbH & Altamira LLC, Nuremberg 90411, Germany
| | - Bruno Bienfait
- MN-AM, Molecular Networks GmbH & Altamira LLC, Nuremberg 90411, Germany
| | - Antony J Williams
- Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Grace Patlewicz
- Center for Computational Toxicology & Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
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30
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Diéguez-Santana K, González-Díaz H. Machine learning in antibacterial discovery and development: A bibliometric and network analysis of research hotspots and trends. Comput Biol Med 2023; 155:106638. [PMID: 36764155 DOI: 10.1016/j.compbiomed.2023.106638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 02/05/2023] [Indexed: 02/10/2023]
Abstract
Machine learning (ML) methods are used in cheminformatics processes to predict the activity of an unknown drug and thus discover new potential antibacterial drugs. This article conducts a bibliometric study to analyse the contributions of leading authors, universities/organisations and countries in terms of productivity, citations and bibliographic linkage. A sample of 1596 Scopus documents for the period 2006-2022 is the basis of the study. In order to develop the analysis, bibliometrix R-Tool and VOSviewer software were used. We determined essential topics related to the application of ML in the field of antibacterial development (Computer model in antibacterial drug design, and Learning algorithms and systems for forecasting). We identified obsolete and saturated areas of research. At the same time, we proposed emerging topics according to the various analyses carried out on the corpus of published scientific literature (Title, abstract and keywords). Finally, the applied methodology contributed to building a broader and more specific "big picture" of ML research in antibacterial studies for the focus of future projects.
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Affiliation(s)
- Karel Diéguez-Santana
- Universidad Regional Amazónica Ikiam, Parroquia Muyuna km 7 vía Alto Tena, 150150, Tena-Napo, Ecuador; Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940, Leioa, Spain.
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, University of Basque Country UPV/EHU, 48940, Leioa, Spain; Basque Center for Biophysics CSIC-UPVEH, University of Basque Country UPV/EHU, 48940, Leioa, Spain; IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Biscay, Spain.
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31
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Andalib KMS, Rahman MH, Habib A. Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer. J Biomol Struct Dyn 2023; 41:14232-14247. [PMID: 36852684 DOI: 10.1080/07391102.2023.2179542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Cervical cancer (CC) is a global threat to women and our knowledge is frighteningly little about its underlying genomic contributors. Our research aimed to understand the underlying molecular and genetic mechanisms of CC by integrating bioinformatics and network-based study. Transcriptomic analyses of three microarray datasets identified 218 common differentially expressed genes (DEGs) within control samples and CC specimens. KEGG pathway analysis revealed pathways in cell cycle, drug metabolism, DNA replication and the significant GO terms were cornification, proteolysis, cell division and DNA replication. Protein-protein interaction (PPI) network analysis identified 20 hub genes and survival analyses validated CDC45, MCM2, PCNA and TOP2A as CC biomarkers. Subsequently, 10 transcriptional factors (TFs) and 10 post-transcriptional regulators were detected through TFs-DEGs and miRNAs-DEGs regulatory network assessment. Finally, the CC biomarkers were subjected to a drug-gene relationship analysis to find the best target inhibitors. Standard cheminformatics method including in silico ADMET and molecular docking study substantiated PD0325901 and Selumetinib as the most potent candidate-drug for CC treatment. Overall, this meticulous study holds promises for further in vitro and in vivo research on CC diagnosis, prognosis and therapies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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32
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Gherman AMR, Dina NE, Chiș V. Cheminformatics Study on Structural and Bactericidal Activity of Latest Generation β-Lactams on Widespread Pathogens. Int J Mol Sci 2022; 23:ijms232012685. [PMID: 36293563 PMCID: PMC9604271 DOI: 10.3390/ijms232012685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 01/24/2023] Open
Abstract
Raman spectra of oxacillin (OXN), carbenicillin (CBC), and azlocillin (AZL) are reported for the first time together with their full assignment of the normal modes, as calculated using Density Functional Theory (DFT) methods with the B3LYP exchange-correlation functional coupled to the 6-31G(d) and 6-311+G(2d,p) basis sets. Molecular docking studies were performed on five penicillins, including OXN, CBC, and AZL. Subsequently, their chemical reactivity and correlated efficiency towards specific pathogenic strains were revealed by combining frontier molecular orbital (FMO) data with molecular electrostatic potential (MEP) surfaces. Their bactericidal activity was tested and confirmed on a couple of species, both Gram-positive and Gram-negative, by using the disk diffusion method. Additionally, a surface-enhanced Raman spectroscopy (SERS)-principal component analysis (PCA)-based resistogram of A. hydrophila is proposed as a clinically relevant insight resulting from the synergistic cheminformatics and vibrational study on CBC and AZL.
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Affiliation(s)
- Ana Maria Raluca Gherman
- Department of Molecular and Biomolecular Physics, National Institute for R&D of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, 400084 Cluj-Napoca, Romania
| | - Nicoleta Elena Dina
- Department of Molecular and Biomolecular Physics, National Institute for R&D of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania
- Correspondence: ; Tel.: +40-264-58-40-37
| | - Vasile Chiș
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, 400084 Cluj-Napoca, Romania
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33
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Khan SA, Khan A, Zia K, Shawish I, Barakat A, Ul-Haq Z. Cheminformatics-Based Discovery of Potential Chemical Probe Inhibitors of Omicron Spike Protein. Int J Mol Sci 2022; 23:ijms231810315. [PMID: 36142242 PMCID: PMC9498999 DOI: 10.3390/ijms231810315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
During the past two decades, the world has witnessed the emergence of various SARS-CoV-2 variants with distinct mutational profiles influencing the global health, economy, and clinical aspects of the COVID-19 pandemic. These variants or mutants have raised major concerns regarding the protection provided by neutralizing monoclonal antibodies and vaccination, rates of virus transmission, and/or the risk of reinfection. The newly emerged Omicron, a genetically distinct lineage of SARS-CoV-2, continues its spread in the face of rising vaccine-induced immunity while maintaining its replication fitness. Efforts have been made to improve the therapeutic interventions and the FDA has issued Emergency Use Authorization for a few monoclonal antibodies and drug treatments for COVID-19. However, the current situation of rapidly spreading Omicron and its lineages demands the need for effective therapeutic interventions to reduce the COVID-19 pandemic. Several experimental studies have indicated that the FDA-approved monoclonal antibodies are less effective than antiviral drugs against the Omicron variant. Thus, in this study, we aim to identify antiviral compounds against the Spike protein of Omicron, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor and facilitates virus invasion. Initially, docking-based virtual screening of the in-house database was performed to extract the potential hit compounds against the Spike protein. The obtained hits were optimized by DFT calculations to determine the electronic properties and molecular reactivity of the compounds. Further, MD simulation studies were carried out to evaluate the dynamics of protein–ligand interactions at an atomistic level in a time-dependent manner. Collectively, five compounds (AKS-01, AKS-02, AKS-03, AKS-04, and AKS-05) with diverse scaffolds were identified as potential hits against the Spike protein of Omicron. Our study paves the way for further in vitro and in vivo studies.
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Affiliation(s)
- Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ihab Shawish
- Department of Math and Sciences, College of Humanities and Sciences, Prince Sultan University, P.O. Box 66833, Riyadh 11586, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Correspondence: (A.B.); (Z.U.-H.)
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Correspondence: (A.B.); (Z.U.-H.)
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Wang Y, Xiong Y, Garcia EAL, Wang Y, Butch CJ. Drug Chemical Space as a Guide for New Herbicide Development: A Cheminformatic Analysis. J Agric Food Chem 2022; 70:9625-9636. [PMID: 35915870 DOI: 10.1021/acs.jafc.2c01425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Herbicides are critical resources for meeting agricultural demand. While similar in structure and function to pharmaceuticals, the development of new herbicidal mechanisms of action and new scaffolds against known mechanisms of action has been much slower than in pharmaceutical sciences. We hypothesized that this may be due in part to a relative undersampling of possible herbicidal chemistries and set out to test whether this difference in sampling existed and whether increasing the diversity of possible herbicidal chemistries would be likely to result in more efficacious herbicides. To conduct this work, we first identified databases of commercially available herbicides and clinically approved pharmaceuticals. Using these databases, we created a two-dimensional embedding of the chemical, which provides a qualitative visualization of the degree to which each chemotype is distributed within the combined chemical space and shows a moderate degree of overlap between the two sets. Next, we trained several machine learning models to classify herbicides versus drugs based on physicochemical characteristics. The most accurate of these models has an accuracy of 93% with the key differentiating characteristics being the number of polar hydrogens, number of amide bonds, LogP, and polar surface area. We then used several types of scaffold decomposition to quantitatively evaluate the chemical diversity of each molecular family and showed herbicides to have considerably fewer unique structural fragments. Finally, we used molecular docking as an in silico evaluation of further structural diversification in herbicide development. To this end, we identified herbicides with well-characterized binding sites and modified those scaffolds based on similar structural subunits from the drug dataset not present in any commercial herbicide while using the machine-learned model to ensure that required herbicide properties were maintained. Redocking the original and modified scaffolds of several herbicides showed that even this simple design strategy is capable of yielding new molecules with higher predicted affinity for the target enzymes. Overall, we show that herbicides are distinct from drugs based on physicochemical properties but less diverse in their chemistry in a way not governed by these properties. We also demonstrate in silico that increasing the diversity of herbicide scaffolds has the potential to increase potency, potentially reducing the amount needed in agricultural practice.
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Affiliation(s)
- Yisheng Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Youjin Xiong
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | | | - Yiqing Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
| | - Christopher J Butch
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China
- Blue Marble Space Institute for Science, Seattle, Washington 98104, United States
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Vanjare BD, Seok Eom Y, Raza H, Hassan M, Hwan Lee K, Ja Kim S. Elastase inhibitory activity of quinoline Analogues: Synthesis, kinetic mechanism, cytotoxicity, chemoinformatics and molecular docking studies. Bioorg Med Chem 2022; 63:116745. [PMID: 35421709 DOI: 10.1016/j.bmc.2022.116745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 11/19/2022]
Abstract
Herein, we have synthesized quinoline united various Schiff base derivatives (Q1-Q13) and systematically characterized them using diverse analytical practices such as 1H NMR, 13C NMR, FT-IR and LC-MS respectively. All of the target compounds that have been synthesized were tested for elastase inhibition, and the findings were compared to the standard drug oleanolic acid. Among the entire series, compound Q11 (IC50 = 0.897 ± 0.015 µM) exhibit most promising elastase inhibitory activity than oleanolic acid (Standard) having an IC50 value of 13.426 ± 0.015 µM. Also, the utmost effectivecompound Q11 was used for kinetic mechanism investigation based on in-vitro data, from which it has been concluded that compound Q11 inhibits elastase competitively. Furthermore, utilizing the MTT test approach, the most effective compounds were assessed for cytotoxicity on B16F10 melanoma cells. From the cytotoxicity experiment, the most potent compound did not display any hazardous response against B16F10 melanoma cells despite being treated at high concentrations. Additionally, the molecular docking study was settled to govern the binding interaction pattern among an enzyme and inhibitors.
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Affiliation(s)
- Balasaheb D Vanjare
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam 32588, Republic of Korea
| | - Young Seok Eom
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam 32588, Republic of Korea
| | - Hussain Raza
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam 32588, Republic of Korea
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Ki Hwan Lee
- Department of Chemistry, Kongju National University, Gongju, Chungnam 32588, Republic of Korea
| | - Song Ja Kim
- Department of Biological Sciences, Kongju National University, Gongju, Chungnam 32588, Republic of Korea.
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Vogt M. Advancing Cheminformatics-A Theme Issue in Honor of Professor Jürgen Bajorath. Molecules 2022; 27:molecules27082542. [PMID: 35458738 PMCID: PMC9028174 DOI: 10.3390/molecules27082542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
While cheminformatics problems have been actively researched since the early 1960s, as witnessed by the QSAR approaches developed by Toshio Fujita and Corwin Hansch [...].
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Affiliation(s)
- 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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Girase R, Ahmad I, Pawara R, Patel H. Optimizing cardio, hepato and phospholipidosis toxicity of the Bedaquiline by chemoinformatics and molecular modelling approach. SAR QSAR Environ Res 2022; 33:215-235. [PMID: 35225110 DOI: 10.1080/1062936x.2022.2041724] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
The FDA granted expedited approval for Johnson and Johnson's Bedaquiline to treat pulmonary multidrug resistant tuberculosis on 28 December 2012 which is more common in China, Russian Federation and India. Bedaquiline is the first anti-tubercular drug approved by the FDA in the last 40 years, and it has become a cynosure in the circles of synthetic chemists researching new anti-tubercular drugs. Bedaquiline's highly lipophilic nature raises major concerns like suppression of the hERG gene, hepatotoxicity, and phospholipidosis despite its potential antitubercular profile. To address these toxicity concerns, in the present work, we have employed the structural optimization of Bedaquiline using the ADMETopt web server, which optimizes lead with scaffold hopping and ADMET screening. The ADMETopt web server yielded the 476 structures through optimization of three sites in Bedaquiline. Further, we have validated the optimized structures for their activity by performing molecular docking and molecular dynamics (MD) simulations against the mycobacterial ATP synthase enzyme and density functional theory (DFT) study further provides insight into the reactivity of the compounds. After screening and analysis, compound #449 was observed to be the most promising mycobacterial ATP synthase inhibitor with minimal cardiotoxicity, hepatotoxicity and phospholipidosis.
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Affiliation(s)
- R Girase
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - I Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - R Pawara
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
| | - H Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur Maharashtra, India
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38
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Leblond A, Houari I, Beauxis Y, Leblanc K, Poupon E, Beniddir MA. Chemoinformatic Exploration of "Bioinspired Metabolomes" Illuminates Diacetyl Assembly Pathways Toward Nesteretal A-Like Cage Molecules. Org Lett 2022; 24:1247-1252. [PMID: 35112872 DOI: 10.1021/acs.orglett.2c00108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An appealing and challenging cage structure along with an unusual biosynthetic pathway prompted us to explore an expeditious bioinspired one-pot total synthesis of nesteretal A. An unconventional strategy was chosen, and a cascade reaction starting from diacetyl was studied. Under organocatalytic conditions mimicking an aldolase, nesteretal A and a related cage analogue were anticipated by in silico metabolization, detected, targeted, and characterized.
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Affiliation(s)
- Axel Leblond
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Inès Houari
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Yann Beauxis
- Université de Paris, CNRS, CiTCoM, F-75006 Paris, France
| | - Karine Leblanc
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Erwan Poupon
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290 Châtenay-Malabry, France
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Flores-Holguín N, Ortega-Castro J, Frau J, Glossman-Mitnik D. Conceptual DFT-Based Computational Peptidology, Pharmacokinetics Study and ADMET Report of the Veraguamides A–G Family of Marine Natural Drugs. Mar Drugs 2022; 20:md20020097. [PMID: 35200627 PMCID: PMC8874632 DOI: 10.3390/md20020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 12/17/2022] Open
Abstract
As a continuation of our research on the chemical reactivity, pharmacokinetics and ADMET properties of cyclopeptides of marine origin with potential therapeutic abilities, in this work our already presented integrated molecular modeling protocol has been used for the study of the chemical reactivity and bioactivity properties of the Veraguamides A–G family of marine natural drugs. This protocol results from the estimation of the conceptual density functional theory (CDFT) chemical reactivity descriptors together with several chemoinformatics tools commonly considered within the process of development of new therapeutic drugs. CP-CDFT is a branch of computational chemistry and molecular modeling dedicated to the study of peptides, and it is a protocol that allows the estimation with great accuracy of the CDFT-based reactivity descriptors and the associated physical and chemical properties, which can aid in determining the ability of the studied peptides to behave as potential useful drugs. Moreover, the superiority of the MN12SX density functional over other long-range corrected density functionals for the prediction of chemical and physical properties in the presence of water as the solvent is clearly demonstrated. The research was supplemented with an investigation of the bioactivity of the molecular systems and their ADMET (absorption, distribution, metabolism, excretion, and toxicity) parameters, as is customary in medicinal chemistry. Some instances of the CDFT-based chemical reactivity descriptors’ capacity to predict the pKas of peptides as well as their potential as AGE inhibitors are also shown.
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Affiliation(s)
- Norma Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Joaquín Ortega-Castro
- Departament de Química, Facultat de Ciènces, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Juan Frau
- Departament de Química, Facultat de Ciènces, Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain; (J.O.-C.); (J.F.)
| | - Daniel Glossman-Mitnik
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
- Correspondence: ; Tel.: +52-614-439-1151
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Krier J, Singh RR, Kondić T, Lai A, Diderich P, Zhang J, Thiessen PA, Bolton EE, Schymanski EL. Discovering pesticides and their TPs in Luxembourg waters using open cheminformatics approaches. Environ Int 2022; 158:106885. [PMID: 34560325 PMCID: PMC8688306 DOI: 10.1016/j.envint.2021.106885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 09/15/2021] [Indexed: 05/05/2023]
Abstract
The diversity of hundreds of thousands of potential organic pollutants and the lack of (publicly available) information about many of them is a huge challenge for environmental sciences, engineering, and regulation. Suspect screening based on high-resolution liquid chromatography-mass spectrometry (LC-HRMS) has enormous potential to help characterize the presence of these chemicals in our environment, enabling the detection of known and newly emerging pollutants, as well as their potential transformation products (TPs). Here, suspect list creation (focusing on pesticides relevant for Luxembourg, incorporating data sources in 4 languages) was coupled to an automated retrieval of related TPs from PubChem based on high confidence suspect hits, to screen for pesticides and their TPs in Luxembourgish river samples. A computational workflow was established to combine LC-HRMS analysis and pre-screening of the suspects (including automated quality control steps), with spectral annotation to determine which pesticides and, in a second step, their related TPs may be present in the samples. The data analysis with Shinyscreen (https://gitlab.lcsb.uni.lu/eci/shinyscreen/), an open source software developed in house, coupled with custom-made scripts, revealed the presence of 162 potential pesticide masses and 96 potential TP masses in the samples. Further identification of these mass matches was performed using the open source approach MetFrag (https://msbi.ipb-halle.de/MetFrag/). Eventual target analysis of 36 suspects resulted in 31 pesticides and TPs confirmed at Level-1 (highest confidence), and five pesticides and TPs not confirmed due to different retention times. Spatio-temporal analysis of the results showed that TPs and pesticides followed similar trends, with a maximum number of potential detections in July. The highest detections were in the rivers Alzette and Mess and the lowest in the Sûre and Eisch. This study (a) added pesticides, classification information and related TPs into the open domain, (b) developed automated open source retrieval methods - both enhancing FAIRness (Findability, Accessibility, Interoperability and Reusability) of the data and methods; and (c) will directly support "L'Administration de la Gestion de l'Eau" on further monitoring steps in Luxembourg.
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Affiliation(s)
- Jessy Krier
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Luxembourg.
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Luxembourg.
| | - Todor Kondić
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Luxembourg.
| | - Adelene Lai
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Luxembourg; Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Lessing Strasse 8, 07743 Jena, Germany.
| | - Philippe Diderich
- Water Management Agency, Ministry of the Environment, Climate and Sustainable Development, 1 Avenue du Rock'n'roll, Luxembourg.
| | - Jian Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Paul A Thiessen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Luxembourg.
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Bayer S, Mayer AI, Borgonovo G, Morini G, Di Pizio A, Bassoli A. Chemoinformatics View on Bitter Taste Receptor Agonists in Food. J Agric Food Chem 2021; 69:13916-13924. [PMID: 34762411 PMCID: PMC8630789 DOI: 10.1021/acs.jafc.1c05057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Food compounds with a bitter taste have a role in human health, both for their capability to influence food choice and preferences and for their possible systemic effect due to the modulation of extra-oral bitter taste receptors (TAS2Rs). Investigating the interaction of bitter food compounds with TAS2Rs is a key step to unravel their complex effects on health and to pave the way to rationally design new additives for food formulation or drugs. Here, we propose a collection of food bitter compounds, for which in vitro activity data against TAS2Rs are available. The patterns of TAS2R subtype-specific agonists were analyzed using scaffold decomposition and chemical space analysis, providing a detailed characterization of the associations between food bitter tastants and TAS2Rs.
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Affiliation(s)
- Sebastian Bayer
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner Str. 34, D-85354 Freising, Germany
- Faculty
of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ariane Isabell Mayer
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
| | - Gigliola Borgonovo
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
| | - Gabriella Morini
- University
of Gastronomic Sciences, piazza Vittorio Emanuele 9, 12042 Pollenzo, (Bra, CN), Italy
| | - Antonella Di Pizio
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner Str. 34, D-85354 Freising, Germany
- . Phone: +49(0)8161716516
| | - Angela Bassoli
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
- . Phone: +39(0)250316815
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Orlov AA, Demenko DY, Bignaud C, Valtz A, Marcou G, Horvath D, Coquelet C, Varnek A, de Meyer F. Chemoinformatics-Driven Design of New Physical Solvents for Selective CO 2 Absorption. Environ Sci Technol 2021; 55:15542-15553. [PMID: 34736317 DOI: 10.1021/acs.est.1c04092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The removal of CO2 from gases is an important industrial process in the transition to a low-carbon economy. The use of selective physical (co-)solvents is especially perspective in cases when the amount of CO2 is large as it enables one to lower the energy requirements for solvent regeneration. However, only a few physical solvents have found industrial application and the design of new ones can pave the way to more efficient gas treatment techniques. Experimental screening of gas solubility is a labor-intensive process, and solubility modeling is a viable strategy to reduce the number of solvents subject to experimental measurements. In this paper, a chemoinformatics-based modeling workflow was applied to build a predictive model for the solubility of CO2 and four other industrially important gases (CO, CH4, H2, and N2). A dataset containing solubilities of gases in 280 solvents was collected from literature sources and supplemented with the new data for six solvents measured in the present study. A modeling workflow based on the usage of several state-of-the-art machine learning algorithms was applied to establish quantitative structure-solubility relationships. The best models were used to perform virtual screening of the industrially produced chemicals. It enabled the identification of compounds with high predicted CO2 solubility and selectivity toward other gases. The prediction for one of the compounds, 4-methylmorpholine, was confirmed experimentally.
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Affiliation(s)
- Alexey A Orlov
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, Strasbourg 67081, France
| | - Daryna Yu Demenko
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, Strasbourg 67081, France
| | - Charles Bignaud
- TotalEnergies S.E., Exploration Production, Development and Support to Operations, Liquefied Natural Gas - Acid Gas Entity, CCUS R&D Program, Paris 92078, France
| | - Alain Valtz
- MINES ParisTech, PSL University, Centre de thermodynamique des procédés (CTP), 35 rue St Honoré, 77300 Fontainebleau, France
| | - Gilles Marcou
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, Strasbourg 67081, France
| | - Dragos Horvath
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, Strasbourg 67081, France
| | - Christophe Coquelet
- MINES ParisTech, PSL University, Centre de thermodynamique des procédés (CTP), 35 rue St Honoré, 77300 Fontainebleau, France
| | - Alexandre Varnek
- Laboratory of Chemoinformatics, Faculty of Chemistry, University of Strasbourg, Strasbourg 67081, France
| | - Frédérick de Meyer
- TotalEnergies S.E., Exploration Production, Development and Support to Operations, Liquefied Natural Gas - Acid Gas Entity, CCUS R&D Program, Paris 92078, France
- MINES ParisTech, PSL University, Centre de thermodynamique des procédés (CTP), 35 rue St Honoré, 77300 Fontainebleau, France
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Flores‐Holguín N, Frau J, Glossman‐Mitnik D. Computational Pharmacokinetics Report, ADMET Study and Conceptual DFT-Based Estimation of the Chemical Reactivity Properties of Marine Cyclopeptides. ChemistryOpen 2021; 10:1142-1149. [PMID: 34806828 PMCID: PMC8607802 DOI: 10.1002/open.202100178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/04/2021] [Indexed: 11/17/2022] Open
Abstract
Homophymines A-E and A1-E1 are bioactive natural cyclodepsipeptides with a complex molecular architecture. These molecules could have a potential use as antimicrobial, antiviral, and anticancer substances. We have carried out a computational study of the properties of this family of marine peptides using a CDFT-based Computational Peptidology (CDFT-CP) methodology that results from the combination of the chemical reactivity descriptors that arise from conceptual Density Functional Theory (CDFT) together with cheminformatics tools. The latter can be used to estimate the associated physicochemical parameters and to improve the process of virtual screening through a similarity search. Using this approach, the ability of the peptides to behave as a potentially useful drugs can be investigated. An analysis of their bioactivity and pharmacokinetics indices related to the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) features has also been carried out.
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Affiliation(s)
- Norma Flores‐Holguín
- Laboratorio Virtual NANOCOSMOSDepartamento de Medio Ambiente y EnergíaCentro de Investigación en Materiales AvanzadosMiguel de Cervantes 120, Complejo Industrial Chihuahua31136Chihuahua, ChihMexico
| | - Juan Frau
- Departament de QuímicaFacultat de CiencesUniversitat de les Illes Balears07122Pama de MallorcaSpain
| | - Daniel Glossman‐Mitnik
- Laboratorio Virtual NANOCOSMOSDepartamento de Medio Ambiente y EnergíaCentro de Investigación en Materiales AvanzadosMiguel de Cervantes 120, Complejo Industrial Chihuahua31136Chihuahua, ChihMexico
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Russo G, Di Salvatore V, Caraci F, Curreli C, Viceconti M, Pappalardo F. How can we accelerate COVID-19 vaccine discovery? Expert Opin Drug Discov 2021; 16:1081-1084. [PMID: 34058925 PMCID: PMC8204312 DOI: 10.1080/17460441.2021.1935861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Giulia Russo
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
- Oasi Research Institute, IRCCS, Troina, Italy
| | - Valentina Di Salvatore
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Filippo Caraci
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
- Oasi Research Institute, IRCCS, Troina, Italy
| | - Cristina Curreli
- Department of Industrial Engineering, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Medical Technology Lab, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Marco Viceconti
- Department of Industrial Engineering, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Medical Technology Lab, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Zhao D, Yi Y, He Q, Wang S, Yang K, Ge J. Exploring the regulatory mechanism of Nao Tai Fang on vascular Dementia's biological network based on cheminformatics and transcriptomics strategy. J Ethnopharmacol 2021; 274:114065. [PMID: 33771644 DOI: 10.1016/j.jep.2021.114065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Nao Tai Fang (NTF) is modified from Buyang Huanwu Decoction. Modern pharmacological research showed that NTF has a good anti-cerebral ischemic effect and can improve the learning and memory ability of cerebrovascular disease. AIM The purpose of this study is to explore the regulation mechanism of NTF on the regulation mechanism of vascular dementia (VD)'s biological network based on chemoinformatics and transcriptomics strategies. METHOD First, the bilateral common carotid artery ligation method was used to create a rat VD model. After NTF intervention for 30 days, the treatment effect was evaluated by HE staining and water maze experiment. Then, the Agilent mRNA expression profiling chip was used to obtain mRNA expression data of hippocampal tissues of VD model rats before and after NTF intervention, and microarray analysis was used to screen for genes with significant differential expression. The BATMAN database was utilized to obtain the potential targets of NTF and the Genecards and OMIM were utilized to collect the VD potential genes. The cytoscape was utilized to construct and analyze the networks. RESULT The animal experiments showed that NTF can improve VD. A total of 180 up-regulated proteins and 289 down-regulated proteins were identified. The top 20 up- and down-regulated differentially expressed genes were utilized to construct differentially expressed gene's protein-protein interaction (PPI) network. A total of 677 NTF potential targets and 550 VD genes were obtained and were utilized to construct NTF-VD PPI network. The cheminformatics analysis showed that NTF can regulate a lot of biological processes and signaling pathways (such as inflammation modules, vasodilation and contraction modules, hypoxia modules, angiogenesis, coagulation, neurovascular unit modules, Neuroactive ligand-receptor interaction, Calcium signaling pathway, Serotonergic synapse). CONCLUSION NTF may play a role in the treatment of VD through the targets, signaling pathways and biological processes discovered in this study.
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Affiliation(s)
- Da Zhao
- Hunan University of Chinese Medicine, Hunan, China
| | - Yaqiao Yi
- Hunan University of Chinese Medicine, Hunan, China
| | - Qi He
- Hunan University of Chinese Medicine, Hunan, China
| | | | - Kailin Yang
- Hunan University of Chinese Medicine, Hunan, China; Capital Medical University, Beijing, China.
| | - Jinwen Ge
- Hunan University of Chinese Medicine, Hunan, China; Shaoyang University, Hunan, China.
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López-López E, Cerda-García-Rojas CM, Medina-Franco JL. Tubulin Inhibitors: A Chemoinformatic Analysis Using Cell-Based Data. Molecules 2021; 26:2483. [PMID: 33923169 PMCID: PMC8123128 DOI: 10.3390/molecules26092483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Inhibiting the tubulin-microtubules (Tub-Mts) system is a classic and rational approach for treating different types of cancers. A large amount of data on inhibitors in the clinic supports Tub-Mts as a validated target. However, most of the inhibitors reported thus far have been developed around common chemical scaffolds covering a narrow region of the chemical space with limited innovation. This manuscript aims to discuss the first activity landscape and scaffold content analysis of an assembled and curated cell-based database of 851 Tub-Mts inhibitors with reported activity against five cancer cell lines and the Tub-Mts system. The structure-bioactivity relationships of the Tub-Mts system inhibitors were further explored using constellations plots. This recently developed methodology enables the rapid but quantitative assessment of analog series enriched with active compounds. The constellations plots identified promising analog series with high average biological activity that could be the starting points of new and more potent Tub-Mts inhibitors.
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Affiliation(s)
- Edgar López-López
- Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico;
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Carlos M. Cerda-García-Rojas
- Departamento de Química y Programa de Posgrado en Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Apartado 14-740, Mexico City 07000, Mexico;
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Shrivastava AD, Kell DB. FragNet, a Contrastive Learning-Based Transformer Model for Clustering, Interpreting, Visualizing, and Navigating Chemical Space. Molecules 2021; 26:2065. [PMID: 33916824 PMCID: PMC8038408 DOI: 10.3390/molecules26072065] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
The question of molecular similarity is core in cheminformatics and is usually assessed via a pairwise comparison based on vectors of properties or molecular fingerprints. We recently exploited variational autoencoders to embed 6M molecules in a chemical space, such that their (Euclidean) distance within the latent space so formed could be assessed within the framework of the entire molecular set. However, the standard objective function used did not seek to manipulate the latent space so as to cluster the molecules based on any perceived similarity. Using a set of some 160,000 molecules of biological relevance, we here bring together three modern elements of deep learning to create a novel and disentangled latent space, viz transformers, contrastive learning, and an embedded autoencoder. The effective dimensionality of the latent space was varied such that clear separation of individual types of molecules could be observed within individual dimensions of the latent space. The capacity of the network was such that many dimensions were not populated at all. As before, we assessed the utility of the representation by comparing clozapine with its near neighbors, and we also did the same for various antibiotics related to flucloxacillin. Transformers, especially when as here coupled with contrastive learning, effectively provide one-shot learning and lead to a successful and disentangled representation of molecular latent spaces that at once uses the entire training set in their construction while allowing "similar" molecules to cluster together in an effective and interpretable way.
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Affiliation(s)
- Aditya Divyakant Shrivastava
- Department of Computer Science and Engineering, Nirma University, Ahmedabad 382481, India;
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Ltd., Liverpool Science Park, IC1, 131 Mount Pleasant, Liverpool L3 5TF, UK
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Ge Y, Li N, Fu Y, Yu X, Xiao Y, Tang Z, Xiao J, Wu JL, Jiang ZH. Deciphering superior quality of Pu-erh tea from thousands of years' old trees based on the chemical profile. Food Chem 2021; 358:129602. [PMID: 33962815 DOI: 10.1016/j.foodchem.2021.129602] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 02/05/2023]
Abstract
Pu-erh teas from thousands of years' old trees (TPT) equip with both superior flavors and powerful antioxidative capacities. With UHPLC-Q-TOF-MS approach, TPTs' chemical profiles were characterized by comparing with Pu-erh teas from ecological trees (EPT). TPTs are discovered to possess higher contents of amino acids, fatty acids, phenolic acids, nucleosides and nucleobases but lower contents of flavonoids and caffeine congeners based on 117 discriminative constituents from 305 identified ones. Particularly, a series of caffeic acid congeners including ten new hydroxycinnamic acid depsides with higher contents in TPTs are discovered, and caffeic acid with a fold change of 638 is the foremost discriminative component. Furthermore, distinguishing constituent proportion including caffeic acid congeners in TPTs are found to take great responsibilities for their more powerful antioxidative abilities and superior flavors especially more aroma and pleasant bitterness. This research provides information for deciphering formation of TPTs' superior qualities based on chemical profile.
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Affiliation(s)
- Yahui Ge
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Yu Fu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Xi Yu
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Ying Xiao
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Zhiying Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region
| | - Jianbo Xiao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region.
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau Special Administrative Region.
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Grigalunas M, Burhop A, Zinken S, Pahl A, Gally JM, Wild N, Mantel Y, Sievers S, Foley DJ, Scheel R, Strohmann C, Antonchick AP, Waldmann H. Natural product fragment combination to performance-diverse pseudo-natural products. Nat Commun 2021; 12:1883. [PMID: 33767198 PMCID: PMC7994817 DOI: 10.1038/s41467-021-22174-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Natural product structure and fragment-based compound development inspire pseudo-natural product design through different combinations of a given natural product fragment set to compound classes expected to be chemically and biologically diverse. We describe the synthetic combination of the fragment-sized natural products quinine, quinidine, sinomenine, and griseofulvin with chromanone or indole-containing fragments to provide a 244-member pseudo-natural product collection. Cheminformatic analyses reveal that the resulting eight pseudo-natural product classes are chemically diverse and share both drug- and natural product-like properties. Unbiased biological evaluation by cell painting demonstrates that bioactivity of pseudo-natural products, guiding natural products, and fragments differ and that combination of different fragments dominates establishment of unique bioactivity. Identification of phenotypic fragment dominance enables design of compound classes with correctly predicted bioactivity. The results demonstrate that fusion of natural product fragments in different combinations and arrangements can provide chemically and biologically diverse pseudo-natural product classes for wider exploration of biologically relevant chemical space.
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Affiliation(s)
- Michael Grigalunas
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Annina Burhop
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Sarah Zinken
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Axel Pahl
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - José-Manuel Gally
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Niklas Wild
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yannik Mantel
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Compound Management and Screening Center, Dortmund, Germany
| | - Daniel J Foley
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- College of Science, University of Canterbury, Canterbury, New Zealand
| | - Rebecca Scheel
- Technical University Dortmund, Faculty of Chemistry and Inorganic Chemistry, Dortmund, Germany
| | - Carsten Strohmann
- Technical University Dortmund, Faculty of Chemistry and Inorganic Chemistry, Dortmund, Germany
| | - Andrey P Antonchick
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- College of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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50
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Dahlin JL, Auld DS, Rothenaigner I, Haney S, Sexton JZ, Nissink JWM, Walsh J, Lee JA, Strelow JM, Willard FS, Ferrins L, Baell JB, Walters MA, Hua BK, Hadian K, Wagner BK. Nuisance compounds in cellular assays. Cell Chem Biol 2021; 28:356-370. [PMID: 33592188 PMCID: PMC7979533 DOI: 10.1016/j.chembiol.2021.01.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Steve Haney
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park SK10 4TG, UK
| | | | | | | | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02140, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA
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