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Irwin BWJ, Vukovic S, Payne MC, Huggins DJ. Large-Scale Study of Hydration Environments through Hydration Sites. J Phys Chem B 2019; 123:4220-4229. [PMID: 31025866 DOI: 10.1021/acs.jpcb.9b02490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hydration sites are locations of interest to water and they can be used to classify the behavior of water around chemical motifs commonly found on the surface of proteins. Inhomogeneous fluid solvation theory (IFST) is a method for calculating hydration free-energy changes from molecular dynamics (MD) trajectories. In this paper, hydration sites are identified from MD simulations of 380 diverse protein structures. The hydration free energies of the hydration sites are calculated using IFST and distributions of these free-energy changes are analyzed. The results show that for some hydration sites near features conventionally regarded as attractive to water, such as hydrogen bond donors, the water molecules are actually relatively weakly bound and are easily displaced. We also construct plots of the spatial density of hydration sites with high, medium, and low hydration free-energy changes which represent weakly and strongly bound hydration sites. It is found that these plots show consistent features around common polar amino acids for all of the proteins studied.
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Affiliation(s)
- Benedict W J Irwin
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Sinisa Vukovic
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - Michael C Payne
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K
| | - David J Huggins
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , U.K.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Department of Physiology and Biophysics , Weill Cornell Medical College , 1300 York Avenue , New York , New York 10065 , United States
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Crooks JE, Boughter CT, Scott LR, Adams EJ. The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution. Front Mol Biosci 2018; 5:95. [PMID: 30483515 PMCID: PMC6243104 DOI: 10.3389/fmolb.2018.00095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/22/2018] [Indexed: 01/12/2023] Open
Abstract
CD4+ and CD8+ αβ T cell antigen recognition is determined by the interaction between the TCR Complementarity Determining Region (CDR) loops and the peptide-presenting MHC complex. These T cells are known for their ability to recognize multiple pMHC complexes, and for a necessary promiscuity that is required for their selection and function in the periphery. Crystallographic studies have previously elucidated the role of structural interactions in TCR engagement, but our understanding of the dynamic process that occurs during TCR binding is limited. To better understand the dynamic states that exist for TCR CDR loops in solution, and how this relates to their states when in complex with pMHC, we simulated the 2C T cell receptor in solution using all-atom molecular dynamics in explicit water and constructed a Markov State Model for each of the CDR3α and CDR3β loops. These models reveal multiple metastable states for the CDR3 loops in solution. Simulation data and metastable states reproduce known CDR3β crystal conformations, and reveal several novel conformations suggesting that CDR3β bound states are the result of search processes from nearby pre-existing equilibrium conformational states. Similar simulations of the invariant, Type I Natural Killer T cell receptor NKT15, which engages the monomorphic, MHC-like CD1d ligand, demonstrate that iNKT TCRs also have distinct states, but comparatively restricted degrees of motion.
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Affiliation(s)
- James E Crooks
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Christopher T Boughter
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - L Ridgway Scott
- Department of Computer Science, University of Chicago, Chicago, IL, United States
| | - Erin J Adams
- Committee on Immunology University of Chicago, Chicago, IL, United States
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Lee KL, Ambler CM, Anderson DR, Boscoe BP, Bree AG, Brodfuehrer JI, Chang JS, Choi C, Chung S, Curran KJ, Day JE, Dehnhardt CM, Dower K, Drozda SE, Frisbie RK, Gavrin LK, Goldberg JA, Han S, Hegen M, Hepworth D, Hope HR, Kamtekar S, Kilty IC, Lee A, Lin LL, Lovering FE, Lowe MD, Mathias JP, Morgan HM, Murphy EA, Papaioannou N, Patny A, Pierce BS, Rao VR, Saiah E, Samardjiev IJ, Samas BM, Shen MWH, Shin JH, Soutter HH, Strohbach JW, Symanowicz PT, Thomason JR, Trzupek JD, Vargas R, Vincent F, Yan J, Zapf CW, Wright SW. Discovery of Clinical Candidate 1-{[(2S,3S,4S)-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design. J Med Chem 2017; 60:5521-5542. [PMID: 28498658 DOI: 10.1021/acs.jmedchem.7b00231] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Through fragment-based drug design focused on engaging the active site of IRAK4 and leveraging three-dimensional topology in a ligand-efficient manner, a micromolar hit identified from a screen of a Pfizer fragment library was optimized to afford IRAK4 inhibitors with nanomolar potency in cellular assays. The medicinal chemistry effort featured the judicious placement of lipophilicity, informed by co-crystal structures with IRAK4 and optimization of ADME properties to deliver clinical candidate PF-06650833 (compound 40). This compound displays a 5-unit increase in lipophilic efficiency from the fragment hit, excellent kinase selectivity, and pharmacokinetic properties suitable for oral administration.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heidi M Morgan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jiangli Yan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
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Drwal MN, Jacquemard C, Perez C, Desaphy J, Kellenberger E. Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? J Chem Inf Model 2017; 57:1197-1209. [PMID: 28414463 DOI: 10.1021/acs.jcim.6b00769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The success of fragment-based drug design (FBDD) hinges upon the optimization of low-molecular-weight compounds (MW < 300 Da) with weak binding affinities to lead compounds with high affinity and selectivity. Usually, structural information from fragment-protein complexes is used to develop ideas about the binding mode of similar but drug-like molecules. In this regard, crystallization additives such as cryoprotectants or buffer components, which are highly abundant in crystal structures, are frequently ignored. Thus, the aim of this study was to investigate the information present in protein complexes with fragments as well as those with additives and how they relate to the binding modes of their drug-like counterparts. We present a thorough analysis of the binding modes of crystallographic additives, fragments, and drug-like ligands bound to four diverse targets of wide interest in drug discovery and highly represented in the Protein Data Bank: cyclin-dependent kinase 2, β-secretase 1, carbonic anhydrase 2, and trypsin. We identified a total of 630 unique molecules bound to the catalytic binding sites, among them 31 additives, 222 fragments, and 377 drug-like ligands. In general, we observed that, independent of the target, protein-fragment interaction patterns are highly similar to those of drug-like ligands and mostly cover the residues crucial for binding. Crystallographic additives are also able to show conserved binding modes and recover the residues important for binding in some of the cases. Moreover, we show evidence that the information from fragments and drug-like ligands can be applied to rescore docking poses in order to improve the prediction of binding modes.
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Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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Zhao LN, Chiu SW, Benoit J, Chew LY, Mu Y. The Effect of Curcumin on the Stability of Aβ Dimers. J Phys Chem B 2012; 116:7428-35. [DOI: 10.1021/jp3034209] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Li Na Zhao
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - See-Wing Chiu
- Beckman Institute, University of Illinois, Urbana, Illinois
| | - Jérôme Benoit
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - Lock Yue Chew
- School of Physical and Mathematical
Sciences, Nanyang Technological University
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive,
Singapore
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Abstract
The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.
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Affiliation(s)
- György G Ferenczy
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, 4. Szt. Gellért tér, Budapest, Hungary, H-1111
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