1
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Duo L, Chen Y, Liu Q, Ma Z, Farjudian A, Ho WY, Low SS, Ren J, Hirst JD, Xie H, Tang B. Discovery of novel SOS1 inhibitors using machine learning. RSC Med Chem 2024; 15:1392-1403. [PMID: 38665844 PMCID: PMC11042245 DOI: 10.1039/d4md00063c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Overactivation of the rat sarcoma virus (RAS) signaling is responsible for 30% of all human malignancies. Son of sevenless 1 (SOS1), a crucial node in the RAS signaling pathway, could modulate RAS activation, offering a promising therapeutic strategy for RAS-driven cancers. Applying machine learning (ML)-based virtual screening (VS) on small-molecule databases, we selected a random forest (RF) regressor for its robustness and performance. Screening was performed with the L-series and EGFR-related datasets, and was extended to the Chinese National Compound Library (CNCL) with more than 1.4 million compounds. In addition to a series of documented SOS1-related molecules, we uncovered nine compounds that have an unexplored chemical framework and displayed inhibitory activity, with the most potent achieving more than 50% inhibition rate in the KRAS G12C/SOS1 PPI assay and an IC50 value in the proximity of 20 μg mL-1. Compared with the manner that known inhibitory agents bind to the target, hit compounds represented by CL01545365 occupy a unique pocket in molecular docking. An in silico drug-likeness assessment suggested that the compound has moderately favorable drug-like properties and pharmacokinetic characteristics. Altogether, our findings strongly support that, characterized by the distinctive binding modes, the recognition of novel skeletons from the carboxylic acid series could be candidates for developing promising SOS1 inhibitors.
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Affiliation(s)
- Lihui Duo
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
| | - Yi Chen
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road 201203 Shanghai China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Qiupei Liu
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road 201203 Shanghai China
| | - Zhangyi Ma
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
| | - Amin Farjudian
- School of Mathematics, Watson Building, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Wan Yong Ho
- Faculty of Medicine and Health Sciences, University of Nottingham (Malaysia Campus) Semenyih 43500 Malaysia
| | - Sze Shin Low
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
| | - Jianfeng Ren
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham University Park Nottingham NG7 2RD UK
| | - Hua Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Road 201203 Shanghai China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Zhongshan Tsuihang New District Zhongshan 528400 China
| | - Bencan Tang
- Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, Department of Chemical and Environmental Engineering, The University of Nottingham Ningbo China 199 Taikang East Road Ningbo 315100 P. R. China
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2
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King TE, Humphrey JR, Laughton CA, Thomas NR, Hirst JD. Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations. J Chem Inf Model 2024; 64:265-275. [PMID: 38113509 PMCID: PMC10777730 DOI: 10.1021/acs.jcim.3c01898] [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: 11/26/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection in solution. In this work, we have explored the relationship between the structure and antiaggregation activity of excipients by utilizing coarse-grained molecular dynamics modeling of protein-excipient interaction. We have studied human serum albumin as a model protein, and we report the interaction of 41 excipients (polysorbates, fatty alcohol ethoxylates, fatty acid ethoxylates, phospholipids, glucosides, amino acids, and others) in terms of the reduction of solvent accessible surface area of aggregation-prone regions, proposed as a mechanism of aggregation prevention. Polyoxyethylene sorbitan had the greatest degree of interaction with aggregation-prone regions, decreasing the solvent accessible surface area of APRs by 20.7 nm2 (40.1%). Physicochemical descriptors generated by Mordred are employed to probe the structure-property relationship using partial least-squares regression. A leave-one-out cross-validated model had a root-mean-square error of prediction of 4.1 nm2 and a mean relative error of prediction of 0.077. Generally, longer molecules with a large number of alcohol-terminated PEG units tended to interact more, with qualitatively different protein interactions, wrapping around the protein. Shorter or less ethoxylated compounds tend to form hemimicellar clusters at the protein surface. We propose that an improved design would feature many short chains of 5 to 10 PEG units in many distinct branches and at least some hydrophobic content in the form of medium-length or greater aliphatic chains (i.e., six or more carbon atoms). The combination of molecular dynamics simulation and quantitative modeling is an important first step in an all-purpose protein-independent model for the computer-aided design of stabilizing excipients.
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Affiliation(s)
- Toby E. King
- Biodiscovery
Institute, School of Pharmacy, University Park, Nottingham NG7 2RD, U.K.
| | | | - Charles A. Laughton
- Biodiscovery
Institute, School of Pharmacy, University Park, Nottingham NG7 2RD, U.K.
| | - Neil R. Thomas
- Biodiscovery
Institute, School of Chemistry, University Park, Nottingham NG7 2RD, U.K.
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3
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Douaki A, Stuber A, Hengsteler J, Momotenko D, Rogers DM, Rocchia W, Hirst JD, Nakatsuka N, Garoli D. Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets. Chem Commun (Camb) 2023; 59:14713-14716. [PMID: 37997814 DOI: 10.1039/d3cc04334g] [Citation(s) in RCA: 1] [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: 11/25/2023]
Abstract
Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo environment with physiological ionic concentrations. In particular, divalent cations (Mg2+ and Ca2+) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.
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Affiliation(s)
- Ali Douaki
- Istituto Italiano di Tecnologia, Via Morego 30, Genova 16136, Italy.
| | - Annina Stuber
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092, Switzerland.
| | - Julian Hengsteler
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092, Switzerland.
| | - Dmitry Momotenko
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26129, Germany
| | - David M Rogers
- School of Chemistry | University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Walter Rocchia
- Istituto Italiano di Tecnologia, Via Morego 30, Genova 16136, Italy.
| | - Jonathan D Hirst
- School of Chemistry | University of Nottingham University Park, Nottingham NG7 2RD, UK
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, CH-8092, Switzerland.
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego 30, Genova 16136, Italy.
- Dip. di Scienze e Metodi dell'Ingegneria, Università di Modena e Reggio Emilia, via Amendola 2, Reggio Emilia 42122, Italy
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4
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Chio H, Guest EE, Hobman JL, Dottorini T, Hirst JD, Stekel DJ. Predicting bioactivity of antibiotic metabolites by molecular docking and dynamics. J Mol Graph Model 2023; 123:108508. [PMID: 37235902 DOI: 10.1016/j.jmgm.2023.108508] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023]
Abstract
Antibiotics enter the environment through waste streams, where they can exert selective pressure for antimicrobial resistance in bacteria. However, many antibiotics are excreted as partly metabolized forms, or can be subject to partial breakdown in wastewater treatment, soil, or through natural processes in the environment. If a metabolite is bioactive, even at sub-lethal levels, and also stable in the environment, then it could provide selection pressure for resistance. (5S)-penicilloic acid of piperacillin has previously been found complexed to the binding pocket of penicillin binding protein 3 (PBP3) of Pseudomonas aeruginosa. Here, we predicted the affinities of all potentially relevant antibiotic metabolites of ten different penicillins to that target protein, using molecular docking and molecular dynamics simulations. Docking predicts that, in addition to penicilloic acid, pseudopenicillin derivatives of these penicillins, as well as 6-aminopenicillanic acid (6APA), could also bind to this target. MD simulations further confirmed that (5R)-pseudopenicillin and 6APA bind the target protein, in addition to (5S)-penicilloic acid. Thus, it is possible that these metabolites are bioactive, and, if stable in the environment, could be contaminants selective for antibiotic resistance. This could have considerable significance for environmental surveillance for antibiotics as a means to reduce antimicrobial resistance, because targeted mass spectrometry could be required for relevant metabolites as well as the native antibiotics.
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Affiliation(s)
- Hokin Chio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Ellen E Guest
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Aukland Park Kingsway Campus, Rossmore, Johannesburg, South Africa.
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5
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Boobier S, Davies JC, Derbenev IN, Handley CM, Hirst JD. AI4Green: An Open-Source ELN for Green and Sustainable Chemistry. J Chem Inf Model 2023; 63:2895-2901. [PMID: 37155346 DOI: 10.1021/acs.jcim.3c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An Electronic Laboratory Notebook (ELN) combining features, including data archival, collaboration tools, and green and sustainability metrics for organic chemistry, is presented. AI4Green is a web-based application, available as open-source code and free to use. It offers the core functionality of an ELN, namely, the ability to store reactions securely and share them among different members of a research team. As users plan their reactions and record them in the ELN, green and sustainable chemistry is encouraged by automatically calculating green metrics and color-coding hazards, solvents, and reaction conditions. The interface links a database constructed from data extracted from PubChem, enabling the automatic collation of information for reactions. The application's design facilitates the development of auxiliary sustainability applications, such as our Solvent Guide. As more reaction data are captured, subsequent work will include providing "intelligent" sustainability suggestions to the user.
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Affiliation(s)
- Samuel Boobier
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Joseph C Davies
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Ivan N Derbenev
- Digital Research Service, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom
| | - Christopher M Handley
- Digital Research Service, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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6
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Redshaw J, Ting DSJ, Brown A, Hirst JD, Gärtner T. Krein support vector machine classification of antimicrobial peptides. Digit Discov 2023; 2:502-511. [PMID: 37065679 PMCID: PMC10087059 DOI: 10.1039/d3dd00004d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023]
Abstract
Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and time-consuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating the discovery process. Kernel methods are a class of machine learning algorithms that utilise a kernel function to transform input data into a new representation. When appropriately normalised, the kernel function can be regarded as a notion of similarity between instances. However, many expressive notions of similarity are not valid kernel functions, meaning they cannot be used with standard kernel methods such as the support-vector machine (SVM). The Kreĭn-SVM represents generalisation of the standard SVM that admits a much larger class of similarity functions. In this study, we propose and develop Kreĭn-SVM models for AMP classification and prediction by employing the Levenshtein distance and local alignment score as sequence similarity functions. Utilising two datasets from the literature, each containing more than 3000 peptides, we train models to predict general antimicrobial activity. Our best models achieve an AUC of 0.967 and 0.863 on the test sets of each respective dataset, outperforming the in-house and literature baselines in both cases. We also curate a dataset of experimentally validated peptides, measured against Staphylococcus aureus and Pseudomonas aeruginosa, in order to evaluate the applicability of our methodology in predicting microbe-specific activity. In this case, our best models achieve an AUC of 0.982 and 0.891, respectively. Models to predict both general and microbe-specific activities are made available as web applications.
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Affiliation(s)
- Joseph Redshaw
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Darren S J Ting
- Academic Ophthalmology, School of Medicine, University of Nottingham Nottingham NG7 2UH UK
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham Birmingham UK
- Birmingham and Midland Eye Centre Birmingham UK
| | - Alex Brown
- Artificial Intelligence and Machine Learning, GSK Medicines Research Centre Gunnels Wood Road Stevenage SG1 2NY UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Thomas Gärtner
- Machine Learning Group, TU Wien Informatics Vienna Austria
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7
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Griffiths RC, Smith FR, Li D, Wyatt J, Rogers DM, Long JE, Cusin LML, Tighe PJ, Layfield R, Hirst JD, Müller MM, Mitchell NJ. Cysteine-Selective Modification of Peptides and Proteins via Desulfurative C-C Bond Formation. Chemistry 2023; 29:e202202503. [PMID: 36534955 PMCID: PMC10946470 DOI: 10.1002/chem.202202503] [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: 08/11/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The site-selective modification of peptides and proteins facilitates the preparation of targeted therapeutic agents and tools to interrogate biochemical pathways. Among the numerous bioconjugation techniques developed to install groups of interest, those that generate C(sp3 )-C(sp3 ) bonds are significantly underrepresented despite affording proteolytically stable, biogenic linkages. Herein, a visible-light-mediated reaction is described that enables the site-selective modification of peptides and proteins via desulfurative C(sp3 )-C(sp3 ) bond formation. The reaction is rapid and high yielding in peptide systems, with comparable translation to proteins. Using this chemistry, a range of moieties is installed into model systems and an effective PTM-mimic is successfully integrated into a recombinantly expressed histone.
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Affiliation(s)
- Rhys C. Griffiths
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Frances R. Smith
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Diyuan Li
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Jasmine Wyatt
- Department of ChemistryKing's College LondonLondonSE1 1DB
| | - David M. Rogers
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Jed E. Long
- School of Life SciencesUniversity of Nottingham Medical SchoolNottinghamNG7 2UHUK
| | - Lola M. L. Cusin
- School of Life SciencesUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Patrick J. Tighe
- School of Life SciencesUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
| | - Robert Layfield
- School of Life SciencesUniversity of Nottingham Medical SchoolNottinghamNG7 2UHUK
| | - Jonathan D. Hirst
- School of ChemistryUniversity of NottinghamUniversity ParkNottinghamNG7 2RDUK
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8
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Davies JC, Pattison D, Hirst JD. Machine learning for yield prediction for chemical reactions using in situ sensors. J Mol Graph Model 2023; 118:108356. [PMID: 36272195 DOI: 10.1016/j.jmgm.2022.108356] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 11/28/2022]
Abstract
Machine learning models were developed to predict product formation from time-series reaction data for ten Buchwald-Hartwig coupling reactions. The data was provided by DeepMatter and was collected in their DigitalGlassware cloud platform. The reaction probe has 12 sensors to measure properties of interest, including temperature, pressure, and colour. Colour was a good predictor of product formation for this reaction and machine learning models were able to learn which of the properties were important. Predictions for the current product formation (in terms of % yield) had a mean absolute error of 1.2%. For predicting 30, 60 and 120 min ahead the error rose to 3.4, 4.1 and 4.6%, respectively. The work here presents an example into the insight that can be obtained from applying machine learning methods to sensor data in synthetic chemistry.
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Affiliation(s)
- Joseph C Davies
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | | | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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9
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Lentz JC, Cavanagh R, Moloney C, Falcone Pin B, Kortsen K, Fowler HR, Jacob PL, Krumins E, Clark C, Machado F, Breitkreuz N, Cale B, Goddard AR, Hirst JD, Taresco V, Howdle SM. N-Hydroxyethyl acrylamide as a functional eROP initiator for the preparation of nanoparticles under "greener" reaction conditions. Polym Chem 2022; 13:6032-6045. [PMID: 36353599 PMCID: PMC9623607 DOI: 10.1039/d2py00849a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
N-Hydroxyethyl acrylamide was used as a functional initiator for the enzymatic ring-opening polymerisation of ε-caprolactone and δ-valerolactone. N-Hydroxyethyl acrylamide was found not to undergo self-reaction in the presence of Lipase B from Candida antarctica under the reaction conditions employed. By contrast, this is a major problem for 2-hydroxyethyl methacrylate and 2-hydroxyethyl acrylate which both show significant transesterification issues leading to unwanted branching and cross-linking. Surprisingly, N-hydroxyethyl acrylamide did not react fully during enzymatic ring-opening polymerisation. Computational docking studies helped us understand that the initiated polymer chains have a higher affinity for the enzyme active site than the initiator alone, leading to polymer propagation proceeding at a faster rate than polymer initiation leading to incomplete initiator consumption. Hydroxyl end group fidelity was confirmed by organocatalytic chain extension with lactide. N-Hydroxyethyl acrylamide initiated polycaprolactones were free-radical copolymerised with PEGMA to produce a small set of amphiphilic copolymers. The amphiphilic polymers were shown to self-assemble into nanoparticles, and to display low cytotoxicity in 2D in vitro experiments. To increase the green credentials of the synthetic strategies, all reactions were carried out in 2-methyl tetrahydrofuran, a solvent derived from renewable resources and an alternative for the more traditionally used fossil-based solvents tetrahydrofuran, dichloromethane, and toluene.
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Affiliation(s)
- Joachim C Lentz
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Robert Cavanagh
- School of Pharmacy, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Cara Moloney
- School of Pharmacy, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Bruno Falcone Pin
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Kristoffer Kortsen
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Harriet R Fowler
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Philippa L Jacob
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Eduards Krumins
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Charlotte Clark
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Fabricio Machado
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
- Institute of Chemistry, University of Brasília Campus Universitário Darcy Ribeiro 70910-900 Brasília DF Brazil
| | - Nicholas Breitkreuz
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Ben Cale
- Croda Europe Limited Cowick Hall Snaith DN14 9AA Goole UK
| | - Amy R Goddard
- Croda Europe Limited Cowick Hall Snaith DN14 9AA Goole UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Vincenzo Taresco
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
| | - Steven M Howdle
- School of Chemistry, University of Nottingham, University Park NG7 2RD Nottingham UK
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10
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Rogers DM, Do H, Hirst JD. Electronic circular dichroism of proteins computed using a diabatisation scheme. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2133748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Affiliation(s)
- David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo, People’s Republic of China
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
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11
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Silva AF, Guest EE, Falcone BN, Pickett SD, Rogers DM, Hirst JD. Free energy perturbation calculations of tetrahydroquinolines complexed to the first bromodomain of BRD4. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2124201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, Nottingham, UK
| | | | - Stephen D. Pickett
- GlaxoSmithKline R&D Pharmaceuticals, Computational Chemistry, Stevenage, UK
| | - David M. Rogers
- School of Chemistry, University of Nottingham, Nottingham, UK
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12
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Abstract
Accurate and rapid predictions of the binding affinity of a compound to a target are one of the ultimate goals of computer aided drug design. Alchemical approaches to free energy estimations follow the path from an initial state of the system to the final state through alchemical changes of the energy function during a molecular dynamics simulation. Herein, we explore the accuracy and efficiency of two such techniques: relative free energy perturbation (FEP) and multisite lambda dynamics (MSλD). These are applied to a series of inhibitors for the bromodomain-containing protein 4 (BRD4). We demonstrate a procedure for obtaining accurate relative binding free energies using MSλD when dealing with a change in the net charge of the ligand. This resulted in an impressive comparison with experiment, with an average difference of 0.4 ± 0.4 kcal mol-1. In a benchmarking study for the relative FEP calculations, we found that using 20 lambda windows with 0.5 ns of equilibration and 1 ns of data collection for each window gave the optimal compromise between accuracy and speed. Overall, relative FEP and MSλD predicted binding free energies with comparable accuracy, an average of 0.6 kcal mol-1 for each method. However, MSλD makes predictions for a larger molecular space over a much shorter time scale than relative FEP, with MSλD requiring a factor of 18 times less simulation time for the entire molecule space.
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Affiliation(s)
- Ellen
E. Guest
- School
of Chemistry, University of Nottingham,
University Park, Nottingham NG7 2RD, U.K.
| | - Luis F. Cervantes
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen D. Pickett
- Computational
Chemistry, GlaxoSmithKline RD Pharmaceuticals, Stevenage SG1 2NY, U.K.
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jonathan D. Hirst
- School
of Chemistry, University of Nottingham,
University Park, Nottingham NG7 2RD, U.K.,
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13
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Gaughan SJH, Hirst JD, Croft AK, Jäger CM. Effect of Oriented Electric Fields on Biologically Relevant Iron-Sulfur Clusters: Tuning Redox Reactivity for Catalysis. J Chem Inf Model 2022; 62:591-601. [PMID: 35045248 DOI: 10.1021/acs.jcim.1c00791] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme-based iron-sulfur clusters, exemplified in families such as hydrogenases, nitrogenases, and radical S-adenosylmethionine enzymes, feature in many essential biological processes. The functionality of biological iron-sulfur clusters extends beyond simple electron transfer, relying primarily on the redox activity of the clusters, with a remarkable diversity for different enzymes. The active-site structure and the electrostatic environment in which the cluster resides direct this redox reactivity. Oriented electric fields in enzymatic active sites can be significantly strong, and understanding the extent of their effect on iron-sulfur cluster reactivity can inform first steps toward rationally engineering their reactivity. An extensive systematic density functional theory-based screening approach using OPBE/TZP has afforded a simple electric field-effect representation. The results demonstrate that the orientation of an external electric field of strength 28.8 MV cm-1 at the center of the cluster can have a significant effect on its relative stability in the order of 35 kJ mol-1. This shows clear implications for the reactivity of iron-sulfur clusters in enzymes. The results also demonstrate that the orientation of the electric field can alter the most stable broken-symmetry state, which further has implications on the directionality of initiated electron-transfer reactions. These insights open the path for manipulating the enzymatic redox reactivity of iron-sulfur cluster-containing enzymes by rationally engineering oriented electric fields within the enzymes.
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Affiliation(s)
- Samuel J H Gaughan
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.,Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Anna K Croft
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Christof M Jäger
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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14
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Zhou J, Wu S, Lee BG, Chen T, He Z, Lei Y, Tang B, Hirst JD. Machine-Learning-Enabled Virtual Screening for Inhibitors of Lysine-Specific Histone Demethylase 1. Molecules 2021; 26:7492. [PMID: 34946572 PMCID: PMC8707381 DOI: 10.3390/molecules26247492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/27/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/01/2022] Open
Abstract
A machine learning approach has been applied to virtual screening for lysine specific demethylase 1 (LSD1) inhibitors. LSD1 is an important anti-cancer target. Machine learning models to predict activity were constructed using Morgan molecular fingerprints. The dataset, consisting of 931 molecules with LSD1 inhibition activity, was obtained from the ChEMBL database. An evaluation of several candidate algorithms on the main dataset revealed that the support vector regressor gave the best model, with a coefficient of determination (R2) of 0.703. Virtual screening, using this model, identified five predicted potent inhibitors from the ZINC database comprising more than 300,000 molecules. The virtual screening recovered a known inhibitor, RN1, as well as four compounds where activity against LSD1 had not previously been suggested. Thus, we performed a machine-learning-enabled virtual screening of LSD1 inhibitors using only the structural information of the molecules.
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Affiliation(s)
- Jiajun Zhou
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Shiying Wu
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Boon Giin Lee
- School of Computer Science, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China;
| | - Tianwei Chen
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Ziqi He
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Yukun Lei
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Bencan Tang
- Key Laboratory for Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100, China; (J.Z.); (S.W.); (T.C.); (Z.H.); (Y.L.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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15
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Correction to Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2021; 121:13698. [PMID: 34709802 DOI: 10.1021/acs.chemrev.1c00758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Haywood AL, Redshaw J, Hanson-Heine MWD, Taylor A, Brown A, Mason AM, Gärtner T, Hirst JD. Kernel Methods for Predicting Yields of Chemical Reactions. J Chem Inf Model 2021; 62:2077-2092. [PMID: 34699222 DOI: 10.1021/acs.jcim.1c00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in regression tasks related to chemical reactivity have often been based on time-consuming, computationally demanding quantum chemical calculations, usually density functional theory. Structure-based descriptors (molecular fingerprints and molecular graphs) are quicker and easier to calculate and are applicable to any molecule. In this study, SVR models built on structure-based descriptors were compared to models built on quantum chemical descriptors. The models were evaluated along the dimension of each reaction component in a set of Buchwald-Hartwig amination reactions. The structure-based SVR models outperformed the quantum chemical SVR models, along the dimension of each reaction component. The applicability of the models was assessed with respect to similarity to training. Prospective predictions of unseen Buchwald-Hartwig reactions are presented for synthetic assessment, to validate the generalizability of the models, with particular interest along the aryl halide dimension.
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Affiliation(s)
- Alexe L Haywood
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Joseph Redshaw
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | | | - Adam Taylor
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Alex Brown
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Andrew M Mason
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Thomas Gärtner
- Machine Learning Research Unit, TU Wien Informatics, Vienna 1040, Austria
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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17
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Affiliation(s)
- Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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18
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Abstract
The bromodomain-containing protein 4 (BRD4), a member of the bromodomain and extra-terminal domain (BET) family, plays a key role in several diseases, especially cancers. With increased interest in BRD4 as a therapeutic target, many X-ray crystal structures of the protein in complex with small molecule inhibitors are publicly available over the recent decade. In this study, we use this structural information to investigate the conformations of the first bromodomain (BD1) of BRD4. Structural alignment of 297 BRD4-BD1 complexes shows a high level of similarity between the structures of BRD4-BD1, regardless of the bound ligand. We employ WONKA, a tool for detailed analyses of protein binding sites, to compare the active site of over 100 of these crystal structures. The positions of key binding site residues show a high level of conformational similarity, with the exception of Trp81. A focused analysis on the highly conserved water network in the binding site of BRD4-BD1 is performed to identify the positions of these water molecules across the crystal structures. The importance of the water network is illustrated using molecular docking and absolute free energy perturbation simulations. 82% of the ligand poses were better predicted when including water molecules as part of the receptor. Our analysis provides guidance for the design of new BRD4-BD1 inhibitors and the selection of the best structure of BRD4-BD1 to use in structure-based drug design, an important approach for faster and more cost-efficient lead discovery.
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Affiliation(s)
- Ellen E Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Stephen D Pickett
- GlaxoSmithKline R&D Pharmaceuticals, Computational Chemistry, Stevenage, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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19
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Robinson D, Alarfaji SS, Hirst JD. Benzene, Toluene, and Monosubstituted Derivatives: Diabatic Nature of the Oscillator Strengths of S 1 ← S 0 Transitions. J Phys Chem A 2021; 125:5237-5245. [PMID: 34132093 PMCID: PMC8279645 DOI: 10.1021/acs.jpca.1c01685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/05/2021] [Indexed: 11/28/2022]
Abstract
For benzene, toluene, aniline, fluorobenzene, and phenol, even sophisticated treatments of electron correlation, such as MRCI and XMS-CASPT2 calculations, show oscillator strengths typically lower than experiment. Inclusion of a simple pseudo-diabatization approach to perturb the S1 state with approximate vibronic coupling to the S2 state for each molecule results in more accurate oscillator strengths. Their absolute values agree better with experiment for all molecules except aniline. When the coupling between the S1 and S2 states is strong at the S0 geometry, the simple diabatization scheme performs less well with respect to the oscillator strengths relative to the adiabatic values. However, we expect the scheme to be useful in many cases where the coupling is weak to moderate (where the maximum component of the coupling has a magnitude less than 1.5 au). Such calculations give an insight into the effects of vibronic coupling of excited states on UV/vis spectra.
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Affiliation(s)
- David Robinson
- Department
of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United
Kingdom
| | - Saleh S. Alarfaji
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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20
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Segatta F, Rogers DM, Dyer NT, Guest EE, Li Z, Do H, Nenov A, Garavelli M, Hirst JD. Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides. Molecules 2021; 26:E396. [PMID: 33451152 PMCID: PMC7828623 DOI: 10.3390/molecules26020396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/09/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.
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Affiliation(s)
- Francesco Segatta
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Naomi T. Dyer
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Ellen E. Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
| | - Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China;
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China;
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari”, Universita’ degli Studi di Bologna, Viale del Risorgimento, 4, I-40136 Bologna, Italy; (F.S.); (A.N.); (M.G.)
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK; (D.M.R.); (N.T.D.); (E.E.G.)
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21
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Pacheco AAC, da Silva Filho AF, Kortsen K, Hanson-Heine MWD, Taresco V, Hirst JD, Lansalot M, D'Agosto F, Howdle SM. Influence of structure and solubility of chain transfer agents on the RAFT control of dispersion polymerisation in scCO 2. Chem Sci 2021; 12:1016-1030. [PMID: 34163868 PMCID: PMC8179044 DOI: 10.1039/d0sc05281g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reversible addition–fragmentation chain transfer (RAFT) dispersion polymerisation of methyl methacrylate (MMA) is performed in supercritical carbon dioxide (scCO2) with 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT) present as chain transfer agent (CTA) and surprisingly shows good control over PMMA molecular weight. Kinetic studies of the polymerisation in scCO2 also confirm these data. By contrast, only poor control of MMA polymerisation is obtained in toluene solution, as would be expected for this CTA which is better suited for acrylates. In this regard, we select a range of CTAs and use them to determine the parameters that must be considered for good control in dispersion polymerisation in scCO2. A thorough investigation of the nucleation stage during the dispersion polymerisation reveals an unexpected “in situ two-stage” mechanism that strongly determines how the CTA works. Finally, using a novel computational solvation model, we identify a correlation between polymerisation control and degree of solubility of the CTAs. All of this ultimately gives rise to a simple, elegant and counterintuitive guideline to select the best CTA for RAFT dispersion polymerisation in scCO2. RAFT dispersion polymerisation of methyl methacrylate is performed in scCO2 with 2-(dodecylthiocarbonothioylthio)-2-methylpropionic acid (DDMAT) present as chain transfer agent (CTA) and surprisingly shows good control over PMMA molecular weight.![]()
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Affiliation(s)
- Ana A. C. Pacheco
- University of Nottingham, University Park, Nottingham, England, NG7 2RD, UK
| | | | - Kristoffer Kortsen
- University of Nottingham, University Park, Nottingham, England, NG7 2RD, UK
| | | | - Vincenzo Taresco
- University of Nottingham, University Park, Nottingham, England, NG7 2RD, UK
| | - Jonathan D. Hirst
- University of Nottingham, University Park, Nottingham, England, NG7 2RD, UK
| | - Muriel Lansalot
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, UMR 5265, Chemistry, Catalysis, Polymers and Processes (C2P2), 43 Bd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Franck D'Agosto
- Univ. Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS, UMR 5265, Chemistry, Catalysis, Polymers and Processes (C2P2), 43 Bd du 11 Novembre 1918, 69616 Villeurbanne, France
| | - Steven M. Howdle
- University of Nottingham, University Park, Nottingham, England, NG7 2RD, UK
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22
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Abstract
The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dynamics (MD) simulations of αvβ6 in complex with its natural ligand, pro-TGF-β1, show the persistence over time of a bidentate Arg-Asp ligand-receptor interaction and a metal chelate interaction between an aspartate on the ligand and an Mg2+ ion in the active site. This is typical of RGD binding ligands. Additional binding site interactions, which are not observed in the static crystal structure, are also identified. We investigate an RGD mimetic, which serves as a framework for a series of potential αvβ6 antagonists. The scaffold includes a derivative of the widely utilized 1,8-naphthyridine moiety, for which we present force field parameters, to enable MD and relative free energy perturbation (FEP) simulations. The MD simulations highlight the importance of hydrogen bonding and cation-π interactions. The FEP calculations predict relative binding affinities, within 1.5 kcal mol-1, on average, of experiments.
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Affiliation(s)
- Ellen E Guest
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Steven A Oatley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | | | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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23
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Solé-Daura A, Rodríguez-Fortea A, Poblet JM, Robinson D, Hirst JD, Carbó JJ. Origin of Selectivity in Protein Hydrolysis by Zr(IV)-Containing Metal Oxides as Artificial Proteases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Albert Solé-Daura
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Antonio Rodríguez-Fortea
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Josep M. Poblet
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - David Robinson
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
- Department of Chemistry and Forensics, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Jorge J. Carbó
- Department de Quı́mica Fı́sica i Inorgànica, Universitat Rovira i Virgili, Marcel·lí Domingo 1, 43007 Tarragona, Spain
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24
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Ye S, Zhong K, Zhang J, Hu W, Hirst JD, Zhang G, Mukamel S, Jiang J. A Machine Learning Protocol for Predicting Protein Infrared Spectra. J Am Chem Soc 2020; 142:19071-19077. [PMID: 33126795 DOI: 10.1021/jacs.0c06530] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations in a fluctuating environment. Herein we present a novel machine learning protocol that uses a few key structural descriptors to rapidly predict amide I IR spectra of various proteins and agrees well with experiment. Its transferability enabled us to distinguish protein secondary structures, probe atomic structure variations with temperature, and monitor protein folding. This approach offers a cost-effective tool to model the relationship between protein spectra and their biological/chemical properties.
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Affiliation(s)
- Sheng Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jinxiao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Wei Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Guozhen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shaul Mukamel
- Departments of Chemistry, and Physics & Astronomy, University of California, Irvine, California 92697, United States
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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25
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Spankie TJ, Haywood AL, Dottorini T, Barrow PA, Hirst JD. Interaction of the maturation protein of the bacteriophage MS2 and the sex pilus of the Escherichia coli F plasmid. J Mol Graph Model 2020; 101:107723. [PMID: 32927271 DOI: 10.1016/j.jmgm.2020.107723] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
One promising strategy to combat antimicrobial resistance is to use bacteriophages that attach to the sex pili produced by transmissible antimicrobial resistance (AMR) plasmids, infect AMR bacteria and select for loss of the AMR plasmids, prolonging the life of existing antimicrobials. The maturation protein of the bacteriophage MS2 attaches to the pili produced by Incompatibility group F plasmid-containing bacteria. This interaction initiates delivery of the viral genetic material into the bacteria. Using protein-protein docking we constructed a model of the F pilus comprising a trimer of subunits binding to the maturation protein. Interactions between the maturation protein and the F pilus were investigated using molecular dynamics simulations. In silico alanine scanning and in silico single-point mutations were explored, with the longer term aim of increasing the affinity of the maturation protein to other Incompatibility group pili, without reducing the strength of binding to F pilin. We report our computational findings on which residues are required for the maturation protein and F pilin to interact, those which had no effect on the interaction and the mutations which led to a stronger interaction.
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Affiliation(s)
- Timothy J Spankie
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Alexe L Haywood
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE125RD, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG72RD, UK.
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26
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Abstract
Calculated circular dichroism spectra in the far- and near-UV spectra. Calculated infra-red (IR) spectra in the amide I region. Based on experimental structures and computational models of SARS-CoV-2 proteins. Near-UV CD spectra offer greatest sensitivity to conformation.
Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models.
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Affiliation(s)
- Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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27
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [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: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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Jiang L, Rogers DM, Hirst JD, Do H. Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene. J Chem Theory Comput 2020; 16:5150-5162. [DOI: 10.1021/acs.jctc.0c00399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ling Jiang
- Department of Chemical and Environmental Engineering, University of Nottingham—Ningbo China, Ningbo 315100, China
| | - David M. Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering, University of Nottingham—Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham—Ningbo China, Ningbo 315042, China
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Abstract
Cyclacene nanobelts have not been synthesized in over 60 years and remain one of the last unsynthesized building blocks of carbon nanotubes. Recent work has predicted that Hückel-cyclacenes containing Dewar benzenoid ring isomers are the most stable isomeric forms for several of the smaller sizes of cyclacene belts. Here, we give a more complete picture of the isomers that are possible within these nanobelt systems by simulating embedded Ladenburg (prismane) benzenoid rings in Hückel-[n]cyclacenes (n = 5-14) and embedded Dewar benzenoid rings in twisted Möbius-[n]cyclacenes (n = 9-14). The Möbius-[9]cyclacene isomer containing one Dewar benzenoid defect and the Hückel-[5]cyclacene isomer containing two maximally spaced Ladenburg benzenoid defects are found to be more stable than their conventional Kekulé benzenoid ring counterparts. The isomers that contain Dewar and Ladenburg benzenoid rings have larger electronic singlet-triplet energy gaps and lower polyradical character when compared with the conventional isomers.
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Affiliation(s)
- Magnus W D Hanson-Heine
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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30
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Abstract
We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.
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Affiliation(s)
- Francois Auvray
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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31
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Robinson H, Oatley SA, Rowedder JE, Slade P, Macdonald SJF, Argent SP, Hirst JD, McInally T, Moody CJ. Late-Stage Functionalization by Chan-Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors. Chemistry 2020; 26:7678-7684. [PMID: 32129907 DOI: 10.1002/chem.202001059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Indexed: 11/07/2022]
Abstract
A late-stage functionalization of the aromatic ring in amino acid derivatives is described. The key step is a copper-catalysed diversification of a boronate ester by amination (Chan-Lam reaction) that can be carried out on a complex β-aryl-β-amino acid scaffold. This not only considerably extends the substrate scope of amination partners, but also delivers an array of potent and selective integrin inhibitors as potential treatment agents of idiopathic pulmonary fibrosis (IPF). This versatile chemical strategy, which is amenable to high-throughput-array protocols, allows the installation of pharmaceutically valuable heteroaromatic fragments at a late stage by direct coupling to NH heterocycles, leading to compounds with drug-like attributes. It thus constitutes a useful addition to the medicinal chemist's repertoire.
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Affiliation(s)
- Henry Robinson
- School of Chemistry, GSK Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Jubilee Campus, Triumph Road, Nottingham, NG7 2TU, UK
| | - Steven A Oatley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - James E Rowedder
- Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Pawel Slade
- Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Simon J F Macdonald
- Medicinal Science & Technology, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Stephen P Argent
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Thomas McInally
- School of Chemistry, GSK Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, Jubilee Campus, Triumph Road, Nottingham, NG7 2TU, UK
| | - Christopher J Moody
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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32
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Abstract
The synthesis of cyclacene nanobelts remains an elusive goal dating back over 60 years. These molecules represent the last unsynthesized building block of carbon nanotubes and may be useful both as seed molecules for the preparation of structurally well-defined carbon nanotubes and for understanding the behavior and formation of zigzag nanotubes more broadly. Here we report the discovery that isomers containing two Dewar benzenoid rings are the preferred form for several sizes of cyclacene. The predicted lower polyradical character and higher singlet-triplet stability that these isomers possess compared with their pure benzenoid counterparts suggest that they may be more stable synthetic targets than the structures that have previously been identified. Our findings should facilitate the exploration of new routes to cyclacene synthesis through Dewar benzene chemistry.
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Affiliation(s)
| | - David M Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Simon Woodward
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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34
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Auvray F, Dennetiere D, Giuliani A, Jamme F, Wien F, Nay B, Zirah S, Polack F, Menneglier C, Lagarde B, Hirst JD, Réfrégiers M. Time resolved transient circular dichroism spectroscopy using synchrotron natural polarization. Struct Dyn 2019; 6:054307. [PMID: 31700943 PMCID: PMC6823104 DOI: 10.1063/1.5120346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Ultraviolet (UV) synchrotron radiation circular dichroism (SRCD) spectroscopy has made an important contribution to the determination and understanding of the structure of bio-molecules. In this paper, we report an innovative approach that we term time-resolved SRCD (tr-SRCD), which overcomes the limitations of current broadband UV SRCD setups. This technique allows accessing ultrafast time scales (down to nanoseconds), previously measurable only by other methods, such as infrared (IR), nuclear magnetic resonance (NMR), fluorescence and absorbance spectroscopies, and small angle X-ray scattering (SAXS). The tr-SRCD setup takes advantage of the natural polarization of the synchrotron radiation emitted by a bending magnet to record broadband UV CD faster than any current SRCD setup, improving the acquisition speed from 10 mHz to 130 Hz and the accessible temporal resolution by several orders of magnitude. We illustrate the new approach by following the isomer concentration changes of an azopeptide after a photoisomerization. This breakthrough in SRCD spectroscopy opens up a wide range of potential applications to the detailed characterization of biological processes, such as protein folding and protein-ligand binding.
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Affiliation(s)
| | - David Dennetiere
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette 91192, France
| | | | - Frédéric Jamme
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette 91192, France
| | - Frank Wien
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette 91192, France
| | - Bastien Nay
- Laboratoire de Synthèse Organique, Ecole Polytechnique, ENSTA-ParisTech, CNRS, Institut Polytechnique de Paris, Route de Saclay, 91128 Palaiseau, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle, CNRS, Paris 75005, France
| | - François Polack
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette 91192, France
| | - Claude Menneglier
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette 91192, France
| | | | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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35
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Hildebrand N, Michaelis M, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Gil-Ley A, Bussi G, Köppen S, Delle Piane M, Ciacchi LC. Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica. ACS Biomater Sci Eng 2018; 4:4036-4050. [DOI: 10.1021/acsbiomaterials.8b00819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Nils Hildebrand
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Monika Michaelis
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Nina Wurzler
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Zhuo Li
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - András Micsonai
- ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - József Kardos
- ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest H-1117, Hungary
| | - Alejandro Gil-Ley
- International School for Advanced Studies (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - Giovanni Bussi
- International School for Advanced Studies (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - Susan Köppen
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Massimo Delle Piane
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science, Center for Environmental Research and Sustainable Technology (UFT), and MAPEX Center for Materials and Processes, University of Bremen, Am Fallturm 1, Bremen 28359, Germany
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36
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Jasim SB, Li Z, Guest EE, Hirst JD. DichroCalc: Improvements in Computing Protein Circular Dichroism Spectroscopy in the Near-Ultraviolet. J Mol Biol 2018; 430:2196-2202. [DOI: 10.1016/j.jmb.2017.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/24/2017] [Accepted: 12/10/2017] [Indexed: 12/13/2022]
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Oglic D, Oatley SA, Macdonald SJF, Mcinally T, Garnett R, Hirst JD, Gärtner T. Active Search for Computer-aided Drug Design. Mol Inform 2018; 37. [PMID: 29388736 DOI: 10.1002/minf.201700130] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/03/2018] [Indexed: 01/08/2023]
Abstract
We consider lead discovery as active search in a space of labelled graphs. In particular, we extend our recent data-driven adaptive Markov chain approach, and evaluate it on a focused drug design problem, where we search for an antagonist of an αv integrin, the target protein that belongs to a group of Arg-Gly-Asp integrin receptors. This group of integrin receptors is thought to play a key role in idiopathic pulmonary fibrosis, a chronic lung disease of significant pharmaceutical interest. As an in silico proxy of the binding affinity, we use a molecular docking score to an experimentally determined αvβ6 protein structure. The search is driven by a probabilistic surrogate of the activity of all molecules from that space. As the process evolves and the algorithm observes the activity scores of the previously designed molecules, the hypothesis of the activity is refined. The algorithm is guaranteed to converge in probability to the best hypothesis from an a priori specified hypothesis space. In our empirical evaluations, the approach achieves a large structural variety of designed molecular structures for which the docking score is better than the desired threshold. Some novel molecules, suggested to be active by the surrogate model, provoke a significant interest from the perspective of medicinal chemistry and warrant prioritization for synthesis. Moreover, the approach discovered 19 out of the 24 active compounds which are known to be active from previous biological assays.
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Affiliation(s)
- Dino Oglic
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom.,Institut für Informatik III, Universität Bonn, Römerstraße 164, 53117, Bonn, Germany
| | - Steven A Oatley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Simon J F Macdonald
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Thomas Mcinally
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Roman Garnett
- Department of Computer Science and Engineering Washington University in St. Louis, One Brookings Drive CB 1045, St. Louis, MO, 63130, USA
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Thomas Gärtner
- School of Computer Science, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham, NG8 1BB, United Kingdom
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38
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Shaw DJ, Hill RE, Simpson N, Husseini FS, Robb K, Greetham GM, Towrie M, Parker AW, Robinson D, Hirst JD, Hoskisson PA, Hunt NT. Examining the role of protein structural dynamics in drug resistance in Mycobacterium tuberculosis. Chem Sci 2017; 8:8384-8399. [PMID: 29619185 PMCID: PMC5863454 DOI: 10.1039/c7sc03336b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/16/2017] [Indexed: 12/12/2022] Open
Abstract
2D-IR spectroscopy reveals a role for protein structural dynamics in antimicrobial-resistance.
Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic–target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from Mycobacterium tuberculosis was studied using ultrafast two-dimensional infrared (2D-IR) spectroscopy and molecular simulations. Comparing wild-type InhA with a series of single point mutations, it was found that binding of the INH–NAD inhibitor to susceptible forms of the enzyme increased the vibrational coupling between residues located in the Rossmann fold co-factor binding site of InhA and suppressed dynamic fluctuations of the enzyme structure. The effect correlated with biochemical assay data, being reduced in the INH-resistant S94A mutant and absent in the biochemically-inactive P193A control. Molecular dynamics simulations and calculations of inter–residue couplings indicate that the changes in coupling and dynamics are not localised to the co-factor binding site, but permeate much of the protein. We thus propose that the resistant S94A mutation circumvents subtle changes in global structural dynamics caused by INH upon binding to the wild-type enzyme that may impact upon the formation of important protein–protein complexes in the fatty acid synthase pathway of M. tuberculosis.
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Affiliation(s)
- Daniel J Shaw
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Rachel E Hill
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Niall Simpson
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
| | - Fouad S Husseini
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Kirsty Robb
- Strathclyde Institute of Pharmacy and Biomedical Science , University of Strathclyde , Glasgow , UK .
| | - Gregory M Greetham
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - Michael Towrie
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - Anthony W Parker
- STFC Central Laser Facility , Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Science and Innovation Campus , Didcot , OX110PE , Oxon , UK
| | - David Robinson
- Department of Chemistry and Forensics , Nottingham Trent University , Clifton Lane , Nottingham , NG11 8NS , UK
| | - Jonathan D Hirst
- School of Chemistry , University of Nottingham , Nottingham , UK .
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Science , University of Strathclyde , Glasgow , UK .
| | - Neil T Hunt
- Department of Physics , University of Strathclyde , SUPA , 107 Rottenrow East , Glasgow , G4 0NG , UK .
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39
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Li Z, Hirst JD. Quantitative first principles calculations of protein circular dichroism in the near-ultraviolet. Chem Sci 2017; 8:4318-4333. [PMID: 29163925 PMCID: PMC5637123 DOI: 10.1039/c7sc00586e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/23/2017] [Indexed: 11/30/2022] Open
Abstract
Vibrational structure in the near-UV circular dichroism (CD) spectra of proteins is an important source of information on protein conformation and can be exploited to study structure and folding. A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper interpretation of and insight into biophysical and simulation studies of protein dynamics and folding. We have developed new models of the aromatic side chain chromophores toluene, p-cresol and 3-methylindole, which incorporate ab initio calculations of the Franck-Condon effect into first principles calculations of CD using an exciton approach. The near-UV CD spectra of 40 proteins are calculated with the new parameter set and the correlation between the computed and the experimental intensity from 270 to 290 nm is much improved. The contribution of individual chromophores to the CD spectra has been calculated for several mutants and in many cases helps rationalize changes in their experimental spectra. Considering conformational flexibility by using families of NMR structures leads to further improvements for some proteins and illustrates an informative level of sensitivity to side chain conformation. In several cases, the near-UV CD calculations can distinguish the native protein structure from a set of computer-generated misfolded decoy structures.
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Affiliation(s)
- Zhuo Li
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
| | - Jonathan D Hirst
- School of Chemistry , University of Nottingham , University Park , Nottingham NG7 2RD , UK .
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Suess CJ, Hirst JD, Besley NA. Quantum chemical calculations of tryptophan → heme electron and excitation energy transfer rates in myoglobin. J Comput Chem 2017; 38:1495-1502. [PMID: 28369976 PMCID: PMC5434924 DOI: 10.1002/jcc.24793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 11/10/2022]
Abstract
The development of optical multidimensional spectroscopic techniques has opened up new possibilities for the study of biological processes. Recently, ultrafast two‐dimensional ultraviolet spectroscopy experiments have determined the rates of tryptophan → heme electron transfer and excitation energy transfer for the two tryptophan residues in myoglobin (Consani et al., Science, 2013, 339, 1586). Here, we show that accurate prediction of these rates can be achieved using Marcus theory in conjunction with time‐dependent density functional theory. Key intermediate residues between the donor and acceptor are identified, and in particular the residues Val68 and Ile75 play a critical role in calculations of the electron coupling matrix elements. Our calculations demonstrate how small changes in structure can have a large effect on the rates, and show that the different rates of electron transfer are dictated by the distance between the heme and tryptophan residues, while for excitation energy transfer the orientation of the tryptophan residues relative to the heme is important. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Christian J Suess
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Nicholas A Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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Husseini FS, Robinson D, Hunt NT, Parker AW, Hirst JD. Computing infrared spectra of proteins using the exciton model. J Comput Chem 2016; 38:1362-1375. [PMID: 27868210 PMCID: PMC5434914 DOI: 10.1002/jcc.24674] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/22/2016] [Accepted: 10/29/2016] [Indexed: 02/02/2023]
Abstract
The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm-1 ) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Fouad S Husseini
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - David Robinson
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Neil T Hunt
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow, G4 0NG, Scotland, United Kingdom
| | - Anthony W Parker
- STFC Rutherford Appleton Laboratory, Central Laser Facility, Harwell Campus, Didcot, OX11 0QX, United Kingdom
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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Solé-Daura A, Goovaerts V, Stroobants K, Absillis G, Jiménez-Lozano P, Poblet JM, Hirst JD, Parac-Vogt TN, Carbó JJ. Cover Picture: Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations (Chem. Eur. J. 43/2016). Chemistry 2016. [DOI: 10.1002/chem.201603456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Albert Solé-Daura
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Vincent Goovaerts
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Karen Stroobants
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Gregory Absillis
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Pablo Jiménez-Lozano
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Jonathan D. Hirst
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Tatjana N. Parac-Vogt
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Jorge J. Carbó
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
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43
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Solé-Daura A, Goovaerts V, Stroobants K, Absillis G, Jiménez-Lozano P, Poblet JM, Hirst JD, Parac-Vogt TN, Carbó JJ. Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations. Chemistry 2016. [DOI: 10.1002/chem.201603740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Albert Solé-Daura
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Vincent Goovaerts
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Karen Stroobants
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Gregory Absillis
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Pablo Jiménez-Lozano
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Jonathan D. Hirst
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD United Kingdom
| | - Tatjana N. Parac-Vogt
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Jorge J. Carbó
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
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Solé-Daura A, Goovaerts V, Stroobants K, Absillis G, Jiménez-Lozano P, Poblet JM, Hirst JD, Parac-Vogt TN, Carbó JJ. Probing Polyoxometalate-Protein Interactions Using Molecular Dynamics Simulations. Chemistry 2016; 22:15280-15289. [DOI: 10.1002/chem.201602263] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Albert Solé-Daura
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Vincent Goovaerts
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Karen Stroobants
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Gregory Absillis
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Pablo Jiménez-Lozano
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Josep M. Poblet
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
| | - Jonathan D. Hirst
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Tatjana N. Parac-Vogt
- Laboratory of Bioinorganic Chemistry; KU Leuven; Celestijnenlaan 200F 3001 Heverlee Belgium
| | - Jorge J. Carbó
- Departament de Química Física i Inorgànica; Universitat Rovira i Virgili; Marcel⋅lí Domingo, 1 43007 Tarragona Spain
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Hanson-Heine MWD, Husseini FS, Hirst JD, Besley NA. Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes. J Chem Theory Comput 2016; 12:1905-18. [DOI: 10.1021/acs.jctc.5b01198] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Fouad S. Husseini
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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Zanni M, Jemmis ED, Aravamudhan S, Arunan E, Hunt N, Mukhopadhyay S, Shepherd HJ, Keshavamurthy S, Dijkstra AG, Ashfold M, Prabal Goswami H, Nenov A, Medhi H, Ghiggino K, Moirangthem K, Miller RJD, Goswami D, Umapathy S, Helliwell JR, Hirst JD, Meech S, Mukamel S, Bagchi B, Buron-Le Cointe M. Local and Global Dynamics: general discussion. Faraday Discuss 2015; 177:381-403. [DOI: 10.1039/c5fd90018b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dhoke K, Zanni M, Harbola U, Venkatraman RK, Arunan E, Lin KC, Nenov A, Skelton J, Miller RJD, Hirst JD, Aquilanti V, Helliwell JR, Keshavamurthy S, Ramesh S, Ashfold M, Pallipurath A, Roy Chowdhury P, Mukhopadhyay S, E D J, Medhi H, Goswami D, Halder P, Junge W, Hariharan M, Singh SK, Umapathy S, Lakshmannam A, Meedom Nielsen M, Aravamudhan S, Deckert V, Ghiggino K, Tominaga K, Edwards A. Dynamics of chemical bond: general discussion. Faraday Discuss 2015; 177:121-54. [DOI: 10.1039/c5fd90016f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
The Franck–Condon effect is considered and the vibrational structure of the πnbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and πnbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the πnbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.
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Affiliation(s)
- Zhuo Li
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
| | - David Robinson
- School of Chemistry
- University of Nottingham
- Nottingham NG7 2RD
- UK
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49
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Zanni M, E D J, Aravamudhan S, Pallipurath A, Arunan E, Schnedermann C, Mishra AK, Warren M, Hirst JD, John F, Pal R, Helliwell JR, Moirangthem K, Chakraborty S, Dijkstra AG, Roy Chowdhury P, Ghiggino K, Miller RJD, Meech S, Medhi H, Hariharan M, Ariese F, Edwards A, Mallia AR, Umapathy S, Meedom Nielsen M, Hunt N, Tian ZY, Skelton J, Sankar G, Goswami D. Time and Space resolved Methods: general discussion. Faraday Discuss 2015; 177:263-92. [DOI: 10.1039/c5fd90017d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Baker JA, Hirst JD. Accelerating electrostatic pair methods on graphical processing units to study molecules in supercritical carbon dioxide. Faraday Discuss 2014; 169:343-57. [PMID: 25340544 DOI: 10.1039/c4fd00012a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Traditionally, electrostatic interactions are modelled using Ewald techniques, which provide a good approximation, but are poorly suited to GPU architectures. We use the GPU versions of the LAMMPS MD package to implement and assess the Wolf summation method. We compute transport and structural properties of pure carbon dioxide and mixtures of carbon dioxide with either methane or difluoromethane. The diffusion of pure carbon dioxide is indistinguishable when using the Wolf summation method instead of PPPM on GPUs. The optimum value of the potential damping parameter, α, is 0.075. We observe a decrease in accuracy when the system polarity increases, yet the method is robust for mildly polar systems. We anticipate the method can be used for a number of techniques, and applied to a variety of systems. Substitution of PPPM can yield a two-fold decrease in the wall-clock time.
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Affiliation(s)
- John A Baker
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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