1
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Green SR, Wilson C, Eadsforth TC, Punekar AS, Tamaki FK, Wood G, Caldwell N, Forte B, Norcross NR, Kiczun M, Post JM, Lopez-Román EM, Engelhart CA, Lukac I, Zuccotto F, Epemolu O, Boshoff HIM, Schnappinger D, Walpole C, Gilbert IH, Read KD, Wyatt PG, Baragaña B. Identification and Optimization of Novel Inhibitors of the Polyketide Synthase 13 Thioesterase Domain with Antitubercular Activity. J Med Chem 2023; 66:15380-15408. [PMID: 37948640 PMCID: PMC10683028 DOI: 10.1021/acs.jmedchem.3c01514] [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: 08/16/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
There is an urgent need for new tuberculosis (TB) treatments, with novel modes of action, to reduce the incidence/mortality of TB and to combat resistance to current treatments. Through both chemical and genetic methodologies, polyketide synthase 13 (Pks13) has been validated as essential for mycobacterial survival and as an attractive target for Mycobacterium tuberculosis growth inhibitors. A benzofuran series of inhibitors that targeted the Pks13 thioesterase domain, failed to progress to preclinical development due to concerns over cardiotoxicity. Herein, we report the identification of a novel oxadiazole series of Pks13 inhibitors, derived from a high-throughput screening hit and structure-guided optimization. This new series binds in the Pks13 thioesterase domain, with a distinct binding mode compared to the benzofuran series. Through iterative rounds of design, assisted by structural information, lead compounds were identified with improved antitubercular potencies (MIC < 1 μM) and in vitro ADMET profiles.
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Affiliation(s)
- Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Thomas C. Eadsforth
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Avinash S. Punekar
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio K. Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Gavin Wood
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Barbara Forte
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Neil R. Norcross
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Michael Kiczun
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - John M. Post
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Medicines R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Iva Lukac
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, QC H4A 3J1, Canada
| | - Ian H. Gilbert
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
| | - Beatriz Baragaña
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.
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2
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Guareschi R, Lukac I, Gilbert IH, Zuccotto F. SophosQM: Accurate Binding Affinity Prediction in Compound Optimization. ACS Omega 2023; 8:15083-15098. [PMID: 37151542 PMCID: PMC10157843 DOI: 10.1021/acsomega.2c08132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/07/2023] [Indexed: 05/09/2023]
Abstract
The optimization of compounds' binding affinity for a biological target is a crucial aspect of the drug development process. Being able to accurately predict binding energies in advance of synthesizing compounds would have a massive impact on the speed of the drug discovery process. The ideal binding affinity prediction method should combine accuracy, reliability, and speed. In this paper, we present SophosQM, a quantum mechanics (QM)-based approach, which can accurately predict the binding affinities of compounds to proteins. The binding affinity predictive models generated by SophosQM are based on the fragment molecular orbital (FMO) method to estimate the enthalpic component of the binding free energy, and a macroscopic descriptor, clog P, is used as an approximation of the entropic component. The affinity prediction is performed using multilinear regression, fitting the experimental values against the FMO-computed enthalpic term and clog P. The quality of the prediction can be assessed in terms of the correlation coefficient between experimental and predicted values. In this work, the method's reliability and accuracy are exemplified by applying SophosQM to 70 compounds binding to six different targets of pharmaceutical relevance. Overall, the results show a very satisfactory performance with a global correlation coefficient in the order of 0.9. Our predictions also show a satisfactory performance compared to data based on free energy perturbation. Finally, SophosQM can also be applied in high-throughput mode by using semiempirical QM methods to evaluate large portions of chemical space, while retaining a good level of accuracy, but decreasing the computing time to just a few seconds per compound.
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3
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Mowbray CE, Braillard S, Glossop PA, Whitlock GA, Jacobs RT, Speake J, Pandi B, Nare B, Maes L, Yardley V, Freund Y, Wall RJ, Carvalho S, Bello D, Van den Kerkhof M, Caljon G, Gilbert IH, Corpas-Lopez V, Lukac I, Patterson S, Zuccotto F, Wyllie S. DNDI-6148: A Novel Benzoxaborole Preclinical Candidate for the Treatment of Visceral Leishmaniasis. J Med Chem 2021; 64:16159-16176. [PMID: 34711050 PMCID: PMC8591608 DOI: 10.1021/acs.jmedchem.1c01437] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 12/30/2022]
Abstract
Visceral leishmaniasis (VL) is a parasitic disease endemic across multiple regions of the world and is fatal if untreated. Current therapies are unsuitable, and there is an urgent need for safe, short-course, and low-cost oral treatments to combat this neglected disease. The benzoxaborole chemotype has previously delivered clinical candidates for the treatment of other parasitic diseases. Here, we describe the development and optimization of this series, leading to the identification of compounds with potent in vitro and in vivo antileishmanial activity. The lead compound (DNDI-6148) combines impressive in vivo efficacy (>98% reduction in parasite burden) with pharmaceutical properties suitable for onward development and an acceptable safety profile. Detailed mode of action studies confirm that DNDI-6148 acts principally through the inhibition of Leishmania cleavage and polyadenylation specificity factor (CPSF3) endonuclease. As a result of these studies and its promising profile, DNDI-6148 has been declared a preclinical candidate for the treatment of VL.
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Affiliation(s)
- Charles E. Mowbray
- Drugs
for Neglected Diseases initiative (DNDi), 15 Chemin Louis-Dunant, 1202 Geneva, Switzerland,
| | - Stéphanie Braillard
- Drugs
for Neglected Diseases initiative (DNDi), 15 Chemin Louis-Dunant, 1202 Geneva, Switzerland
| | - Paul A. Glossop
- Sandexis
Medicinal Chemistry Ltd, Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent CT13 9ND, U.K.
| | - Gavin A. Whitlock
- Sandexis
Medicinal Chemistry Ltd, Innovation House, Discovery Park, Ramsgate Road, Sandwich, Kent CT13 9ND, U.K.
| | - Robert T. Jacobs
- Scynexis, 3501 C Tricenter Boulevard, Durham, North Carolina 27713, United States
| | - Jason Speake
- Scynexis, 3501 C Tricenter Boulevard, Durham, North Carolina 27713, United States
| | - Bharathi Pandi
- Scynexis, 3501 C Tricenter Boulevard, Durham, North Carolina 27713, United States
| | - Bakela Nare
- Scynexis, 3501 C Tricenter Boulevard, Durham, North Carolina 27713, United States
| | - Louis Maes
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Vanessa Yardley
- Faculty
of Infectious and Tropical Diseases, London
School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, U.K.
| | - Yvonne Freund
- Anacor Pharmaceuticals, 1020 East Meadow Circle, Palo Alto, California 94303, United States
| | - Richard J. Wall
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Sandra Carvalho
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Davide Bello
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Magali Van den Kerkhof
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Guy Caljon
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Ian H. Gilbert
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Victoriano Corpas-Lopez
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Iva Lukac
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Stephen Patterson
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Fabio Zuccotto
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.
| | - Susan Wyllie
- Division
of Biological Chemistry and Drug Discovery, Wellcome Centre for Anti-infectives
Research, School of Life Sciences, University
of Dundee, Dow Street, Dundee DD1
5EH, U.K.,
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4
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Lukac I, Wyatt PG, Gilbert IH, Zuccotto F. Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method. J Comput Aided Mol Des 2021; 35:1025-1036. [PMID: 34458939 PMCID: PMC8523014 DOI: 10.1007/s10822-021-00416-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022]
Abstract
Water molecules play a crucial role in protein-ligand binding, and many tools exist that aim to predict the position and relative energies of these important, but challenging participants of biomolecular recognition. The available tools are, in general, capable of predicting the location of water molecules. However, predicting the effects of their displacement is still very challenging. In this work, a linear-scaling quantum mechanics-based approach was used to assess water network energetics and the changes in network stability upon ligand structural modifications. This approach offers a valuable way to improve understanding of SAR data and help guide compound design.
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Affiliation(s)
- Iva Lukac
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Paul G Wyatt
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Ian H Gilbert
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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5
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Thomas M, Brand S, De Rycker M, Zuccotto F, Lukac I, Dodd PG, Ko EJ, Manthri S, McGonagle K, Osuna-Cabello M, Riley J, Pont C, Simeons F, Stojanovski L, Thomas J, Thompson S, Viayna E, Fiandor JM, Martin J, Wyatt PG, Miles TJ, Read KD, Marco M, Gilbert IH. Scaffold-Hopping Strategy on a Series of Proteasome Inhibitors Led to a Preclinical Candidate for the Treatment of Visceral Leishmaniasis. J Med Chem 2021; 64:5905-5930. [PMID: 33904304 PMCID: PMC8154566 DOI: 10.1021/acs.jmedchem.1c00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 01/05/2023]
Abstract
![]()
There
is an urgent need for new treatments for visceral leishmaniasis
(VL), a parasitic infection which impacts heavily large areas of East
Africa, Asia, and South America. We previously reported on the discovery
of GSK3494245/DDD01305143 (1) as a preclinical candidate
for VL and, herein, we report on the medicinal chemistry program that
led to its identification. A hit from a phenotypic screen was optimized
to give a compound with in vivo efficacy, which was
hampered by poor solubility and genotoxicity. The work on the original
scaffold failed to lead to developable compounds, so an extensive
scaffold-hopping exercise involving medicinal chemistry design, in silico profiling, and subsequent synthesis was utilized,
leading to the preclinical candidate. The compound was shown to act
via proteasome inhibition, and we report on the modeling of different
scaffolds into a cryo-EM structure and the impact this has on our
understanding of the series’ structure–activity relationships.
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Affiliation(s)
- Michael Thomas
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Stephen Brand
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Manu De Rycker
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Fabio Zuccotto
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Iva Lukac
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Peter G Dodd
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Eun-Jung Ko
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Sujatha Manthri
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Kate McGonagle
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Jennifer Riley
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Caterina Pont
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Frederick Simeons
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Laste Stojanovski
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - John Thomas
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Stephen Thompson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Elisabet Viayna
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Jose M Fiandor
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Julio Martin
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Paul G Wyatt
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Timothy J Miles
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Kevin D Read
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
| | - Maria Marco
- Global Health R&D, GlaxoSmithKline, Tres Cantos 28760, Spain
| | - Ian H Gilbert
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry, University of Dundee, Dundee DD1 5EH, U.K
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6
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Zarnecka J, Lukac I, Messham SJ, Hussin A, Coppola F, Enoch SJ, Dossetter AG, Griffen EJ, Leach AG. Mapping Ligand-Shape Space for Protein-Ligand Systems: Distinguishing Key-in-Lock and Hand-in-Glove Proteins. J Chem Inf Model 2021; 61:1859-1874. [PMID: 33755448 DOI: 10.1021/acs.jcim.1c00089] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many of the recently developed methods to study the shape of molecules permit one conformation of one molecule to be compared to another conformation of the same or a different molecule: a relative shape. Other methods provide an absolute description of the shape of a conformation that does not rely on comparisons or overlays. Any absolute description of shape can be used to generate a self-organizing map (shape map) that places all molecular shapes relative to one another; in the studies reported here, the shape fingerprint and ultrafast shape recognition methods are employed to create such maps. In the shape maps, molecules that are near one another have similar shapes, and the maps for the 102 targets in the DUD-E set have been generated. By examining the distribution of actives in comparison with their physical-property-matched decoys, we show that the proteins of key-in-lock type (relatively rigid receptor and ligand) can be distinguished from those that are more of a hand-in-glove type (more flexible receptor and ligand). These are linked to known differences in protein flexibility and binding-site size.
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Affiliation(s)
- Joanna Zarnecka
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Iva Lukac
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Stephen J Messham
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Alhusein Hussin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | - Francesco Coppola
- Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Steven J Enoch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K
| | | | - Edward J Griffen
- MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, U.K.,MedChemica Limited, Biohub, Mereside, Alderley Park, Macclesfield SK10 4TG, U.K.,Division of Pharmacy and Optometry, School of Health Sciences, University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
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7
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Lukac I, Abdelhakim H, Ward RA, St-Gallay SA, Madden JC, Leach AG. Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A. Chem Sci 2019; 10:2218-2227. [PMID: 30881647 PMCID: PMC6388092 DOI: 10.1039/c8sc04564j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Accurately computing the geometry and energy of host-guest and protein-ligand interactions requires a physically accurate description of the forces in action. Quantum mechanics can provide this accuracy but the calculations can require a prohibitive quantity of computational resources. The size of the calculations can be reduced by including only the atoms of the receptor that are in close proximity to the ligand. We show that when combined with log P values for the ligand (which can be computed easily) this approach can significantly improve the agreement between computed and measured binding energies. When the approach is applied to lactate dehydrogenase A, it can make quantitative predictions about conformational, tautomeric and protonation state preferences as well as stereoselectivity and even identifies potential errors in structures deposited in the Protein Data Bank for this enzyme. By broadening the evidence base for these structures from only the diffraction data, more chemically realistic structures can be proposed.
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Affiliation(s)
- Iva Lukac
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Hend Abdelhakim
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Richard A Ward
- Chemistry, Oncology, IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Stephen A St-Gallay
- Sygnature Discovery Ltd , Bio City, Pennyfoot St , Nottingham , NG1 1GF , UK
| | - Judith C Madden
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
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8
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Lukac I, Zarnecka J, Griffen EJ, Dossetter AG, St-Gallay SA, Enoch SJ, Madden JC, Leach AG. Turbocharging Matched Molecular Pair Analysis: Optimizing the Identification and Analysis of Pairs. J Chem Inf Model 2017; 57:2424-2436. [DOI: 10.1021/acs.jcim.7b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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)
- Iva Lukac
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Joanna Zarnecka
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | | | | | | | - Steven J. Enoch
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Judith C. Madden
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
| | - Andrew G. Leach
- School
of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, U.K
- MedChemica Ltd., BioHub, Alderley
Park, Macclesfield SK10
4TG, U.K
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9
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Barker C, Lukac I, Leach AG. Designing Hydroxamates and Reversed Hydroxamates to Inhibit Zinc-containing Proteases but not Cytochrome P450s: Insights from Quantum Mechanics and Protein-ligand Crystal Structures. Mol Inform 2016; 34:608-14. [PMID: 27490712 DOI: 10.1002/minf.201400171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 03/30/2015] [Accepted: 05/08/2015] [Indexed: 11/07/2022]
Abstract
The Hydroxamate is a useful functional group that binds to metals in a range of enzymes, notably zinc in matrix metalloproteases and histone deacetylases. The group is also able to form interactions with iron leading to inhibition of the cytochromes P450, particularly the 3A4 isoform. We have studied the available crystal structures of zinc-containing proteins bound to hydroxamates and compared the observed geometries with those found by quantum mechanical calculations. This has revealed the likely binding mode preferences for neutral and anionic protonation states and highlighted the importance of electrostatic complementarity. Calculations were also performed for the interaction of the hydroxamate with iron in a heme environment, as found in the cytochromes P450. These reveal that the preferred binding mode of hydroxamates in this environment involves the s-trans conformation. These calculations provide design guidelines for those interested in designing inhibitors of metalloenzymes that do not block metabolism of other drugs. The ability to predict the geometries and energies of binding modes that cannot be studied experimentally is an advantage offered by this kind of study.
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Affiliation(s)
- Charlotte Barker
- Charlotte Barker, Iva Lukac, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Iva Lukac
- Charlotte Barker, Iva Lukac, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Andrew G Leach
- Andrew G. Leach, School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK phone:+44 (0)1512312404.
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Prkacin I, Balenovic D, Djermanovic-Dobrota V, Lukac I, Drazic P, Pranjic IK. Resistant hypertension and chronotherapy. Mater Sociomed 2015; 27:118-21. [PMID: 26005390 PMCID: PMC4404987 DOI: 10.5455/msm.2015.27.118-121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 04/05/2015] [Indexed: 12/02/2022] Open
Abstract
Resistant hypertension is defined as blood pressure that remains above 140/90 mmHg in spite of the continuous use of three antihypertensive agents in optimal dose, including diuretic, and lifestyle changes. According to data from United States of America and Europe, the prevalence ranges from 10 up to 30% in patients with hypertension. Numerous biological and lifestyle factors can contribute to the development of resistant hypertension: medications, volume overload, obesity, diabetes mellitus, older age, renal parenchymal and renovascular disease, primary aldosteronism, obstructive sleep apnea, pheochormocytoma, Cushing’s syndrome, thyroid diseases, aortic coarctation. For diagnosing patient’s history is important, assessing compliance, regular blood pressure measurement, physical examination, biochemical evaluation and noninvasive imaging. The evaluation including 24h ambulatory monitoring of blood pressure (ABPM) in the identification of “non-dipper” hypertension. Non-dipper has particular importance and the prevalence of abnormally high sleep blood pressure is very often in chronic kidney patients. Therapeutic restoration of normal physiologic blood pressure reduction during night-time sleep (circadial variation) is the most significant independent predictor of decreased risk and the basis for the chronotherapy. The resistant hypertension treatment is achieved with nonpharmacological and pharmacological approach, treating secondary hypertension causes and invasive procedures.
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Affiliation(s)
- Ingrid Prkacin
- Merkur University Hospital, Department of Internal Medicine, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Diana Balenovic
- General Hospital Sisak, Department of Internal Medicine, Sisak, Croatia
| | - Vesna Djermanovic-Dobrota
- Merkur University Hospital, Department of Internal Medicine, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Iva Lukac
- Merkur University Hospital, Department of Internal Medicine, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Petra Drazic
- Merkur University Hospital, Department of Internal Medicine, University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Iva-Klara Pranjic
- General Hospital Zadar, Department of Emergency Medicine, Zadar, Croatia
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Girod M, Enjalbert Q, Brunet C, Antoine R, Lemoine J, Lukac I, Radman M, Krisko A, Dugourd P. Structural basis of protein oxidation resistance: a lysozyme study. PLoS One 2014; 9:e101642. [PMID: 24999730 PMCID: PMC4085010 DOI: 10.1371/journal.pone.0101642] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
Accumulation of oxidative damage in proteins correlates with aging since it can cause irreversible and progressive degeneration of almost all cellular functions. Apparently, native protein structures have evolved intrinsic resistance to oxidation since perfectly folded proteins are, by large most robust. Here we explore the structural basis of protein resistance to radiation-induced oxidation using chicken egg white lysozyme in the native and misfolded form. We study the differential resistance to oxidative damage of six different parts of native and misfolded lysozyme by a targeted tandem/mass spectrometry approach of its tryptic fragments. The decay of the amount of each lysozyme fragment with increasing radiation dose is found to be a two steps process, characterized by a double exponential evolution of their amounts: the first one can be largely attributed to oxidation of specific amino acids, while the second one corresponds to further degradation of the protein. By correlating these results to the structural parameters computed from molecular dynamics (MD) simulations, we find the protein parts with increased root-mean-square deviation (RMSD) to be more susceptible to modifications. In addition, involvement of amino acid side-chains in hydrogen bonds has a protective effect against oxidation Increased exposure to solvent of individual amino acid side chains correlates with high susceptibility to oxidative and other modifications like side chain fragmentation. Generally, while none of the structural parameters alone can account for the fate of peptides during radiation, together they provide an insight into the relationship between protein structure and susceptibility to oxidation.
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Affiliation(s)
- Marion Girod
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Quentin Enjalbert
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Brunet
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Rodolphe Antoine
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, 69622, Lyon, France
- Institut des Sciences Analytiques, UMR 5280, CNRS, Université Claude Bernard Lyon 1, Lyon, France
| | - Iva Lukac
- Mediterranean Institute for Life Sciences, Split, Croatia
- Liverpool John Moores University, School of Pharmacy and Biomolecular Sciences, Liverpool, Merseyside, England
| | - Miroslav Radman
- Mediterranean Institute for Life Sciences, Split, Croatia
- INSERM U1001, Faculte de Medecine, Universite R. Descartes Paris-5, Paris, France
| | - Anita Krisko
- Mediterranean Institute for Life Sciences, Split, Croatia
- * E-mail: (PD) (AK); (AK) (PD)
| | - Philippe Dugourd
- Université de Lyon, 69622, Lyon, France
- Institut Lumière Matière, UMR 5306, CNRS, Université Claude Bernard Lyon 1, Lyon, France
- * E-mail: (PD) (AK); (AK) (PD)
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Hrdlovic P, Scaiano JC, Lukac I, Guillet JE. Transient spectroscopy and kinetics of poly(1-(4-substituted-phenyl)-2-propen-1-ones). Macromolecules 2002. [DOI: 10.1021/ma00160a026] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Stojanović S, Lukac I. [Modern radiologic diagnosis of prostatic diseases]. Med Pregl 1996; 49:459-463. [PMID: 9019628] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Prostatic pathology presents one of the key elements of morbidity in adult and older males. In developed countries malignant prostatic tumors are the third most common cause of death in males older than 55 years of age. New diagnostic procedures such as transabdominal and transrectal ultrasound, computerized tomography and magnetic resonance enable direct prostatic visualization thus better and more efficient diagnostics. This study offers a review and schedule of diagnostic procedures which enable early detection and classification of prostatic diseases.
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Affiliation(s)
- S Stojanović
- Zavod za radiologiju, Institut medicinskih sluzbi, Medicinski fakultet, Novi Sad
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Marinković S, Stojanović S, Lukac I, Cvejanov M, Borisev V, Peković-Zrnić V. [Ultrasonographic verification of hypertrophic pyloric stenosis]. Med Pregl 1993; 46:280-281. [PMID: 7968826] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In a two-year study on 24 newborn infants, diagnosis of hypertrophic pyloric stenosis (HPS) was intraoperatively confirmed, following preoperative ultrasonography. By means of real time sonography three parameters of the pyloric muscle were measured; the mean length was 19.6 mm, diameter 13.4 mm and the muscle thickness was 5.1 mm.
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Affiliation(s)
- S Marinković
- Institut za adravstvenu zastitu majke i deteta, Medicinski fakultet, Novi Sad
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Berić B, Miljković S, Lukac I, Gavanski K. [Modern diagnosis of genito-pelvic echinococcosis in women]. Jugosl Ginekol Opstet 1984; 24:100-1. [PMID: 6399086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
From 1927 to 1983, out of 25,388 laparotomies, 10 cases (0.038%), and out of 1,463 vaginal hysterectomies, only one case (0.068%) of genito-pelvic echinococcosis were recorded. Ultrasound (exemplified by a case), and computerized tomography have recently been used for establishing preoperative diagnosis.
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