1
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Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. Eur J Med Chem 2024; 271:116357. [PMID: 38636130 DOI: 10.1016/j.ejmech.2024.116357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/20/2024]
Abstract
The oxindole scaffold has been the center of several kinase drug discovery programs, some of which have led to approved medicines. A series of two oxindole matched pairs from the literature were identified where TLK2 was potently inhibited as an off-target kinase. The oxindole has long been considered a promiscuous kinase inhibitor template, but across these four specific literature oxindoles TLK2 activity was consistent, while the kinome profile was radically different ranging from narrow to broad spectrum kinome coverage. We synthesized a large series of analogues, utilizing quantitative structure-activity relationship (QSAR) analysis, water mapping of the kinase ATP binding sites, kinome profiling, and small-molecule x-ray structural analysis to optimize TLK2 inhibition and kinome selectivity. This resulted in the identification of several narrow spectrum, sub-family selective, chemical tool compounds including 128 (UNC-CA2-103) that could enable elucidation of TLK2 biology.
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Affiliation(s)
- Christopher R M Asquith
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland; Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Michael P East
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carla Alamillo-Ferrer
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Erkka Hartikainen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Carrow I Wells
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Graham J Tizzard
- UK National Crystallography Service, School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Timothy M Willson
- Structural Genomics Consortium and Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gary L Johnson
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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Kaczor AA, Zięba A, Matosiuk D. The application of WaterMap-guided structure-based virtual screening in novel drug discovery. Expert Opin Drug Discov 2024; 19:73-83. [PMID: 37807912 DOI: 10.1080/17460441.2023.2267015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface. AREAS COVERED In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023. EXPERT OPINION In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
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Abd Emoniem N, Mukhtar RM, Ghaboosh H, Elshamly EM, Mohamed MA, Elsaman T, Alzain AA. Turning down PI3K/AKT/mTOR signalling pathway by natural products: an in silico multi-target approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:163-182. [PMID: 36853097 DOI: 10.1080/1062936x.2023.2181392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The PI3K/AKT/mTOR pathway is a significant target for cancer drug discovery. Many efforts have focused on discovering new inhibitors against key kinase proteins involved in this pathway for cancer treatment. PI3K/mTOR dual inhibitors, such as PKI-179, have been reported to be more effective than agents that act only on a single protein target. The present computational study aimed to discover triple target inhibitors against PI3K, AKT, and mTOR proteins. Accordingly, the PI3K protein bound with the ligand was used as input for e-pharmacophore modelling to generate the pharmacophore hypothesis and then screened for a library of 270,540 natural products from the Zinc database resulting in 57,220 compounds that matched the hypothesis. These compounds were then docked into the active site of PI3K, resulting in 292 compounds with better docking scores than the co-crystallized ligand. These compounds were re-docked into AKT and mTOR proteins. Besides, MM-GBSA binding free energy calculations, MD simulations, and ADMET prediction were carried out, leading to 5 potential triple-target inhibitors namely, ZINC000014644152, ZINC000014760695, ZINC000014644839, ZINC000095099451, and ZINC000005998557. In conclusion, these inhibitors may be possible leads for inhibiting PI3K/AKT/mTOR pathway, and they may be further evaluated in vitro and clinically as anticancer agents.
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Affiliation(s)
- N Abd Emoniem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - R M Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - H Ghaboosh
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - E M Elshamly
- Department of Molecular Biotechnology, Hochschule Anhalt, Köthen, Germany
| | - M A Mohamed
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - T Elsaman
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - A A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Dilebo KB, Gumede NJ, Nxumalo W, Matsebatlela TM, Mangokoana D, Moraone NR, Omondi B, Mampa RM. Synthesis, in vitro cytotoxic, anti-Mycobacterium tuberculosis and molecular docking studies of 4-pyridylamino- and 4-(ethynylpyridine)quinazolines. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Andreev S, Pantsar T, Tesch R, Kahlke N, El-Gokha A, Ansideri F, Grätz L, Romasco J, Sita G, Geibel C, Lämmerhofer M, Tarozzi A, Knapp S, Laufer SA, Koch P. Addressing a Trapped High-Energy Water: Design and Synthesis of Highly Potent Pyrimidoindole-Based Glycogen Synthase Kinase-3β Inhibitors. J Med Chem 2021; 65:1283-1301. [PMID: 34213342 DOI: 10.1021/acs.jmedchem.0c02146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In small molecule binding, water is not a passive bystander but rather takes an active role in the binding site, which may be decisive for the potency of the inhibitor. Here, by addressing a high-energy water, we improved the IC50 value of our co-crystallized glycogen synthase kinase-3β (GSK-3β) inhibitor by nearly two orders of magnitude. Surprisingly, our results demonstrate that this high-energy water was not displaced by our potent inhibitor (S)-3-(3-((7-ethynyl-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)piperidin-1-yl)propanenitrile ((S)-15, IC50 value of 6 nM). Instead, only a subtle shift in the location of this water molecule resulted in a dramatic decrease in the energy of this high-energy hydration site, as shown by the WaterMap analysis combined with microsecond timescale molecular dynamics simulations. (S)-15 demonstrated both a favorable kinome selectivity profile and target engagement in a cellular environment and reduced GSK-3 autophosphorylation in neuronal SH-SY5Y cells. Overall, our findings highlight that even a slight adjustment in the location of a high-energy water can be decisive for ligand binding.
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Affiliation(s)
- Stanislav Andreev
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Roberta Tesch
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Niclas Kahlke
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Ahmed El-Gokha
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Chemistry Department, Faculty of Science, Menoufia University, Gamal Abdel-Nasser Street, 32511 Shebin El-Kom, Egypt
| | - Francesco Ansideri
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lukas Grätz
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jenny Romasco
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Giulia Sita
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Christian Geibel
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Stefan A Laufer
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery (TüCAD2), Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Pierre Koch
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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7
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Sabbah DA, Hajjo R, Bardaweel SK, Zhong HA. Phosphatidylinositol 3-kinase (PI3K) inhibitors: a recent update on inhibitor design and clinical trials (2016-2020). Expert Opin Ther Pat 2021; 31:877-892. [PMID: 33970742 DOI: 10.1080/13543776.2021.1924150] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: The phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway plays a central role in regulating cell growth and proliferation and thus has been considered as effective anticancer drug targets. Many PI3K inhibitors have been developed and progressed to various stages of clinical trials, and some have been approved as anticancer treatment. In this review, we discuss the drug design and clinical development of PI3K inhibitors over the past 4 years. We review the selectivity and potency of 47 PI3K inhibitors. Structural determinants for increasing selectivity toward PI3K subtype-selectivity or mutant selectivity are discussed. Future research direction and current clinical development in combination therapy of inhibitors involved in PI3Ks are also discussed.Area covered: This review covers clinical trial reports and patent literature on PI3K inhibitors and their selectivity published between 2016 and 2020.Expert opinion: To PI3Kα mutants (E542K, E545K, and H1047R), it is highly desirable to design and develop mutant-specific PI3K inhibitors. It is also necessary to develop subtype-selective PI3Kα inhibitors to minimize toxicity. To reduce drug resistance and to improve efficacy, future studies should include combination therapy of PI3K inhibitors with existing anticancer drugs from different pathways.
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Affiliation(s)
- Dima A Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
| | - Sanaa K Bardaweel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Jordan, Amman, Jordan
| | - Haizhen A Zhong
- DSC 362, Department of Chemistry, The University of Nebraska at Omaha, Omaha, Nebraska, USA
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8
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Current and Future Challenges in Modern Drug Discovery. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2114:1-17. [PMID: 32016883 DOI: 10.1007/978-1-0716-0282-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Drug discovery is an expensive, time-consuming, and risky business. To avoid late-stage failure, learnings from past projects and the development of new approaches are crucial. New modalities and emerging new target spaces allow the exploration of unprecedented indications or to address so far undrugable targets. Late-stage attrition is usually attributed to the lack of efficacy or to compound-related safety issues. Efficacy has been shown to be related to a strong genetic link to human disease, a better understanding of the target biology, and the availability of biomarkers to bridge from animals to humans. Compound safety can be improved by ligand optimization, which is becoming increasingly demanding for difficult targets. Therefore, new strategies include the design of allosteric ligands, covalent binders, and other modalities. Design methods currently heavily rely on artificial intelligence and advanced computational methods such as free energy calculations and quantum chemistry. Especially for quantum chemical methods, a more detailed overview is given in this chapter.
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Tiwari AP, Sridhar B, Boshoff HI, Arora K, Gautham Shenoy G, Vandana KE, Varadaraj Bhat G. Design, synthesis, in silico and in vitro evaluation of novel diphenyl ether derivatives as potential antitubercular agents. Mol Divers 2020; 24:1265-1279. [PMID: 31506871 PMCID: PMC11177332 DOI: 10.1007/s11030-019-09990-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/24/2019] [Indexed: 11/28/2022]
Abstract
Diphenyl ether derivatives inhibit mycobacterial cell wall synthesis by inhibiting an enzyme, enoyl-acyl carrier protein reductase (InhA), which catalyses the last step in the fatty acid synthesis cycle of genus Mycobacterium. To select and validate a protein crystal structure of enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis for designing inhibitors using molecular modelling, a cross-docking and correlation study was performed. A series of novel 1-(3-(3-hydroxy-4-phenoxyphenyl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl) ethan-1-ones were synthesized from this model and screened for their antitubercular activity against M. tuberculosis H37Rv. Compound PYN-8 showed good antitubercular activity on M. tuberculosis H37Rv (MIC = 4-7 µM) and Mycobacterium bovis (% inhibition at 10 µM = 95.91%). Cytotoxicity of all the synthesized derivatives was assessed using various cell lines, and they were found to be safe. Structure of PYN-8 was also confirmed by single-crystal X-ray diffraction. The molecular modelling studies also corroborated the biological activity of the compounds. Further, in silico findings revealed that all these tested compounds exhibited good ADME properties and drug likeness and thus may be considered as potential candidates for further drug development.
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Affiliation(s)
- Ashutosh Prasad Tiwari
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - B Sridhar
- X-ray Crystallography Division, CSIR - Indian Institute of Chemical Technology, Hyderabad, 500607, India
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G Gautham Shenoy
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - K E Vandana
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, India
| | - G Varadaraj Bhat
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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Asquith CRM, Tizzard GJ, Bennett JM, Wells CI, Elkins JM, Willson TM, Poso A, Laitinen T. Targeting the Water Network in Cyclin G‐Associated Kinase (GAK) with 4‐Anilino‐quin(az)oline Inhibitors. ChemMedChem 2020; 15:1200-1215. [DOI: 10.1002/cmdc.202000150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Christopher R. M. Asquith
- Department of Pharmacology, School of MedicineUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Graham J. Tizzard
- UK National Crystallography Service, School of ChemistryUniversity of Southampton Southampton SO17 1BJ UK
| | - James M. Bennett
- Structural Genomics Consortium and Target Discovery Institute Nuffield Department of Clinical MedicineUniversity of Oxford Old Road Campus Research Building Oxford OX3 7DQ UK)
| | - Carrow I. Wells
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Jonathan M. Elkins
- Structural Genomics Consortium and Target Discovery Institute Nuffield Department of Clinical MedicineUniversity of Oxford Old Road Campus Research Building Oxford OX3 7DQ UK)
- Structural Genomics ConsortiumUniversidade Estadual de Campinas – UNICAMP Campinas São Paulo 13083-886 Brazil
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel Hill Chapel Hill NC 27599 USA
| | - Antti Poso
- School of Pharmacy, Faculty of Health SciencesUniversity of Eastern Finland 70211 Kuopio Finland
- University Hospital Tübingen Department of Internal Medicine VIIIUniversity of Tübingen 72076 Tübingen Germany
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health SciencesUniversity of Eastern Finland 70211 Kuopio Finland
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11
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Dong TG, Peng H, He XF, Wang X, Gao J. Hybrid Molecular Dynamics for Elucidating Cooperativity Between Halogen Bond and Water Molecules During the Interaction of p53-Y220C and the PhiKan5196 Complex. Front Chem 2020; 8:344. [PMID: 32457871 PMCID: PMC7221198 DOI: 10.3389/fchem.2020.00344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/02/2020] [Indexed: 12/15/2022] Open
Abstract
The cooperativity between hydrogen and halogen bonds plays an important role in rational drug design. However, mimicking the dynamic cooperation between these bonds is a challenging issue, which has impeded the development of the halogen bond force field. In this study, the Y220C–PhiKan5196 complex of p53 protein was adopted as a model, and the functions of three water molecules that formed hydrogen bonds with halogen atoms were analyzed by the simulation method governed by the hybrid quantum mechanical/molecular mechanical molecular dynamics. A comparison with the water-free model revealed that the strength of the halogen bond in the complex was consistently stronger. This confirmed that the water molecules formed weak hydrogen bonds with the halogen atom and cooperated with the halogen atom to enhance the halogen bond. Further, it was discovered that the roles of the three water molecules were not the same. Therefore, the results obtained herein can facilitate a rational drug design. Further, this work emphasizes on the fact that, in addition to protein pockets and ligands, the role of voids should also be considered with regard to the water molecules surrounding them.
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Affiliation(s)
- Tian-Ge Dong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Hui Peng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xue-Feng He
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xiaocong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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12
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Wang Q, Wang P, Gao X, Wang D, Wang S, Liang X, Wang L, Zhang H, Lei A. Regioselective/electro-oxidative intermolecular [3 + 2] annulation for the preparation of indolines. Chem Sci 2020; 11:2181-2186. [PMID: 34123309 PMCID: PMC8150106 DOI: 10.1039/c9sc05729c] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Compared with the reported intramolecular electro-oxidative cyclization of alkenyl amines or vinyl anilines for the preparation of pyrrolidines or indolines, the intermolecular version is less studied. Herein, this electrochemical intermolecular oxidative annulation of anilines and alkenes for the preparation of indolines proceeded under external oxidant-free conditions. The most noteworthy achievement of our work is the facile generation of indolines with quaternary centers at the 2-position. In addition, alkenes and anilines bearing various functional groups can be well tolerated. Remarkably, electrolyte-free conditions were used in an electrochemical flow cell, which shows the application potential of this method.
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Affiliation(s)
- Qingqing Wang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Pan Wang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Xinlong Gao
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Dan Wang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Shengchun Wang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Xingan Liang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Liwei Wang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Heng Zhang
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China
| | - Aiwen Lei
- College of Chemistry and Molecular Sciences, Institute for Advanced Studies (IAS), Wuhan University Wuhan 430072 P. R. China .,National Research Center for Carbohydrate Synthesis, Jiangxi Normal University Nanchang 330022 P. R. China
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13
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Bodnarchuk MS, Packer MJ, Haywood A. Utilizing Grand Canonical Monte Carlo Methods in Drug Discovery. ACS Med Chem Lett 2020; 11:77-82. [PMID: 31938467 DOI: 10.1021/acsmedchemlett.9b00499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
The concepts behind targeting waters for potency and selectivity gains have been well documented and explored, although maximizing such potential gains can prove to be challenging. This problem is exacerbated in cases where there are multiple interacting waters, wherein perturbation of one water can affect the free energy landscape of the remaining waters. Knowing the right modification a priori is challenging, and computational approaches are ideally suited to help answer the key question of which substitution is best to try. Here, we use Grand Canonical Monte Carlo and the recent Grand Canonical Alchemical Perturbation methods to both understand and predict the effect of ligand-mediated water displacement when more than one water molecule is involved, as well as to understand how exploiting water networks can help govern selectivity.
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Affiliation(s)
- Michael S. Bodnarchuk
- Computational Chemistry, R&D Oncology, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Martin J. Packer
- Computational Chemistry, R&D Oncology, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Alexe Haywood
- Computational Chemistry, R&D Oncology, AstraZeneca, Cambridge CB4 0WG, United Kingdom
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14
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Wang H, Gao Y, Wang J, Cheng M. Computational Strategy Revealing the Structural Determinant of Ligand Selectivity towards Highly Similar Protein Targets. Curr Drug Targets 2019; 21:76-88. [PMID: 31556854 DOI: 10.2174/1389450120666190926113524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Poor selectivity of drug candidates may lead to toxicity and side effects accounting for as high as 60% failure rate, thus, the selectivity is consistently significant and challenging for drug discovery. OBJECTIVE To find highly specific small molecules towards very similar protein targets, multiple strategies are always employed, including (1) To make use of the diverse shape of binding pocket to avoid steric bump; (2) To increase binding affinities for favorite residues; (3) To achieve selectivity through allosteric regulation of target; (4) To stabalize the inactive conformation of protein target and (5) To occupy dual binding pockets of single target. CONCLUSION In this review, we summarize computational strategies along with examples of their successful applications in designing selective ligands, with the aim to provide insights into everdiversifying drug development practice and inspire medicinal chemists to utilize computational strategies to avoid potential side effects due to low selectivity of ligands.
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Affiliation(s)
- Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Yinli Gao
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning, China
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15
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Kersten C, Fleischer E, Kehrein J, Borek C, Jaenicke E, Sotriffer C, Brenk R. How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study Using N-Myristoyltransferases as a Model System. J Med Chem 2019; 63:2095-2113. [PMID: 31423787 DOI: 10.1021/acs.jmedchem.9b00586] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A model system of two related enzymes with conserved binding sites, namely N-myristoyltransferase from two different organisms, was studied to decipher the driving forces that lead to selective inhibition in such cases. Using a combination of computational and experimental tools, two different selectivity-determining features were identified. For some ligands, a change in side-chain flexibility appears to be responsible for selective inhibition. Remarkably, this was observed for residues orienting their side chains away from the ligands. For other ligands, selectivity is caused by interfering with a water molecule that binds more strongly to the off-target than to the target. On the basis of this finding, a virtual screen for selective compounds was conducted, resulting in three hit compounds with the desired selectivity profile. This study delivers a guideline on how to assess selectivity-determining features in proteins with conserved binding sites and to translate this knowledge into the design of selective inhibitors.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020 Bergen, Norway
| | - Edmond Fleischer
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Josef Kehrein
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020 Bergen, Norway.,Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christoph Borek
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Elmar Jaenicke
- Institute of Molecular Biophysics, Johannes Gutenberg University, Jakob-Welder-Weg 26, 55128 Mainz, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5020 Bergen, Norway
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16
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Design of selective PI3Kδ inhibitors using an iterative scaffold-hopping workflow. Bioorg Med Chem Lett 2019; 29:2575-2580. [PMID: 31416665 DOI: 10.1016/j.bmcl.2019.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/21/2022]
Abstract
PI3Kδ mediates key immune cell signaling pathways and is a target of interest for multiple indications in immunology and oncology. Here we report a structure-based scaffold-hopping strategy for the design of chemically diverse PI3Kδ inhibitors. Using this strategy, we identified several scaffolds that can be combined to generate new PI3Kδ inhibitors with high potency and isoform selectivity. In particular, an oxindole-based scaffold was found to impart exquisite selectivity when combined with several hinge binding motifs.
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17
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Miller MS, Thompson PE, Gabelli SB. Structural Determinants of Isoform Selectivity in PI3K Inhibitors. Biomolecules 2019; 9:biom9030082. [PMID: 30813656 PMCID: PMC6468644 DOI: 10.3390/biom9030082] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) are important therapeutic targets for the treatment of cancer, thrombosis, and inflammatory and immune diseases. The four highly homologous Class I isoforms, PI3K, PI3K, PI3K and PI3K have unique, non-redundant physiological roles and as such, isoform selectivity has been a key consideration driving inhibitor design and development. In this review, we discuss the structural biology of PI3Ks and how our growing knowledge of structure has influenced the medicinal chemistry of PI3K inhibitors. We present an analysis of the available structure-selectivity-activity relationship data to highlight key insights into how the various regions of the PI3K binding site influence isoform selectivity. The picture that emerges is one that is far from simple and emphasizes the complex nature of protein-inhibitor binding, involving protein flexibility, energetics, water networks and interactions with non-conserved residues.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Philip E Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia.
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Medicine, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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18
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Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
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19
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Matter H, Güssregen S. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands. Bioorg Med Chem Lett 2018; 28:2343-2352. [PMID: 29880400 DOI: 10.1016/j.bmcl.2018.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022]
Abstract
Water is an essential part of protein binding sites and mediates interactions to ligands. Its displacement by ligand parts affects the free binding energy of resulting protein-ligand complexes. Therefore the characterization of solvation properties is important for design. Of particular interest is the propensity of localized water to be favorably displaced by a ligand. This review discusses two popular computational approaches addressing these questions, namely WaterMap based on statistical mechanics analysis of MD simulations and 3D RISM based on integral equation theory of liquids. The theoretical background and recent applications in structure-based design will be presented.
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Affiliation(s)
- Hans Matter
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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20
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Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC. Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Commun Chem 2018; 1:19. [PMID: 29863194 PMCID: PMC5978690 DOI: 10.1038/s42004-018-0019-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/01/2018] [Indexed: 12/17/2022] Open
Abstract
Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands and in some cases, contribute towards selectivity. Bromodomains, small protein domains involved in the epigenetic regulation of gene transcription, display a network of four conserved water molecules in their binding pockets and have recently been the focus of intense medicinal chemistry efforts. Understanding why certain bromodomains have displaceable water molecules and others do not is extremely challenging, and it remains unclear which water molecules in a given bromodomain can be targeted for displacement. Here we estimate the stability of the conserved water molecules in 35 bromodomains via binding free energy calculations using all-atom grand canonical Monte Carlo simulations. Encouraging quantitative agreement to the available experimental evidence is found. We thus discuss the expected ease of water displacement in different bromodomains and the implications for ligand selectivity.
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Affiliation(s)
- Matteo Aldeghi
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Michael J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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21
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Ni Y, Yu Q, Liu Q, Zuo H, Yu HB, Wei WJ, Liao RZ, Zhong F. Iron-Catalyzed Regiospecific Intermolecular Radical Cyclization of Anilines: Strategy for Assembly of 2,2-Disubstituted Indolines. Org Lett 2018; 20:1404-1408. [DOI: 10.1021/acs.orglett.8b00176] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yang Ni
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Qile Yu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Qihao Liu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Honghua Zuo
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Huai-Bin Yu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Wen-Jie Wei
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Rong-Zhen Liao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
| | - Fangrui Zhong
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan 430074, China
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22
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Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J Chem Inf Model 2017; 57:2911-2937. [PMID: 29243483 DOI: 10.1021/acs.jcim.7b00564] [Citation(s) in RCA: 391] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives, using a combination of retrospective literature examples and prospective studies from drug discovery projects. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative binding free energy simulations, with a focus on real-world drug discovery applications. We offer guidelines for improving the accuracy of RBFE simulations, especially for challenging cases, and emphasize unresolved issues that could be improved by further research in the field.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens , 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Bryce Allen
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
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23
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Kang NS, Kang YK. Assessment of CCSD(T), MP2, and DFT methods for the calculations of structures and interaction energies of the peptide backbone with water molecules. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Bertoldo JB, Rodrigues T, Dunsmore L, Aprile FA, Marques MC, Rosado LA, Boutureira O, Steinbrecher TB, Sherman W, Corzana F, Terenzi H, Bernardes GJL. A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases. Chem 2017; 3:665-677. [PMID: 29094109 PMCID: PMC5656095 DOI: 10.1016/j.chempr.2017.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 06/01/2017] [Accepted: 07/07/2017] [Indexed: 11/25/2022]
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) strains highlights the need to develop more efficacious and potent drugs. However, this goal is dependent on a comprehensive understanding of Mtb virulence protein effectors at the molecular level. Here, we used a post-expression cysteine (Cys)-to-dehydrolanine (Dha) chemical editing strategy to identify a water-mediated motif that modulates accessibility of the protein tyrosine phosphatase A (PtpA) catalytic pocket. Importantly, this water-mediated Cys-Cys non-covalent motif is also present in the phosphatase SptpA from Staphylococcus aureus, which suggests a potentially preserved structural feature among bacterial tyrosine phosphatases. The identification of this structural water provides insight into the known resistance of Mtb PtpA to the oxidative conditions that prevail within an infected host macrophage. This strategy could be applied to extend the understanding of the dynamics and function(s) of proteins in their native state and ultimately aid in the design of small-molecule modulators.
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Affiliation(s)
- Jean B Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Tiago Rodrigues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Lavinia Dunsmore
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Marta C Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Leonardo A Rosado
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Omar Boutureira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Woody Sherman
- Schrödinger, 120 West 45th Street, New York, NY 10036, USA
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis-SC, Brazil
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisbon, Portugal
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25
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Probst D, Heitz M, Poirier M, Gan BH, Delalande C, Reymond JL. Frontiers in Medicinal Chemistry 2017 in Bern, Switzerland. ChemMedChem 2017; 12:1645-1651. [PMID: 28941184 DOI: 10.1002/cmdc.201700306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Indexed: 11/06/2022]
Abstract
Sharing capital ideas: The 2017 Frontiers in Medicinal Chemistry (FiMC) conference, organized jointly by the German Chemical Society, the German Pharmaceutical Society, and the Swiss Chemical Society, was held at the Department of Chemistry and Biochemistry of the University of Bern in February 2017. Herein we summarize the many conference highlights, and look forward to the next FiMC meeting, to be held in Jena (Germany) in March 2018.
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Affiliation(s)
- Daniel Probst
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marc Heitz
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Marion Poirier
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Bee Ha Gan
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Clémence Delalande
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
| | - Jean-Louis Reymond
- Universität Bern, Departement für Chemie und Biochemie, Freiestrasse 3, Bern, 3012, Switzerland
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26
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Fernández A, Scott LR. Advanced Modeling Reconciles Counterintuitive Decisions in Lead Optimization. Trends Biotechnol 2017; 35:490-497. [DOI: 10.1016/j.tibtech.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
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27
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Hylsová M, Carbain B, Fanfrlík J, Musilová L, Haldar S, Köprülüoğlu C, Ajani H, Brahmkshatriya PS, Jorda R, Kryštof V, Hobza P, Echalier A, Paruch K, Lepšík M. Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines. Eur J Med Chem 2016; 126:1118-1128. [PMID: 28039837 DOI: 10.1016/j.ejmech.2016.12.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 12/17/2022]
Abstract
We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R2 = 0.49). However, the addition of the active-site waters resulted in significant improvement (R2 = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.
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Affiliation(s)
- Michaela Hylsová
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Benoit Carbain
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Lenka Musilová
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Susanta Haldar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Cemal Köprülüoğlu
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Haresh Ajani
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Pathik S Brahmkshatriya
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Radek Jorda
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Vladimír Kryštof
- Laboratory of Growth Regulators, Faculty of Science, Palacký University, Institute of Experimental Botany, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic; Regional Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Aude Echalier
- Centre de Biochimie Structurale, CNRS UMR 5048 - UM - INSERM U 1054, 29 rue de Navacelles, 34090 Montpellier, France
| | - Kamil Paruch
- Department of Chemistry, CZ Openscreen, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic.
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.
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AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. Molecules 2016; 21:molecules21111604. [PMID: 27886114 PMCID: PMC6274120 DOI: 10.3390/molecules21111604] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 11/27/2022] Open
Abstract
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.
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McRobb FM, Negri A, Beuming T, Sherman W. Molecular dynamics techniques for modeling G protein-coupled receptors. Curr Opin Pharmacol 2016; 30:69-75. [DOI: 10.1016/j.coph.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Accepted: 07/03/2016] [Indexed: 11/17/2022]
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