1
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Beyens O, De Winter H. Preventing lipophilic aggregation in cosolvent molecular dynamics simulations with hydrophobic probes using Plumed Automatic Restraining Tool (PART). J Cheminform 2024; 16:23. [PMID: 38414037 PMCID: PMC10898161 DOI: 10.1186/s13321-024-00819-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/23/2024] [Indexed: 02/29/2024] Open
Abstract
Cosolvent molecular dynamics (MD) simulations are molecular dynamics simulations used to identify preferable locations of small organic fragments on a protein target. Most cosolvent molecular dynamics workflows make use of only water-soluble fragments, as hydrophobic fragments would cause lipophilic aggregation. To date the two approaches that allow usage of hydrophobic cosolvent molecules are to use a low (0.2 M) concentration of hydrophobic probes, with the disadvantage of a lower sampling speed, or to use force field modifications, with the disadvantage of a difficult and inflexible setup procedure. Here we present a third alternative, that does not suffer from low sampling speed nor from cumbersome preparation procedures. We have built an easy-to-use open source command line tool PART (Plumed Automatic Restraining Tool) to generate a PLUMED file handling all intermolecular restraints to prevent lipophilic aggregation. We have compared restrained and unrestrained cosolvent MD simulations, showing that restraints are necessary to prevent lipophilic aggregation at hydrophobic probe concentrations of 0.5 M. Furthermore, we benchmarked PART generated restraints on a test set of four proteins (Factor-Xa, HIV protease, P38 MAP kinase and RNase A), showing that cosolvent MD with PART generated restraints qualitatively reproduces binding features of cocrystallised ligands.
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Affiliation(s)
- Olivier Beyens
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
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2
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Li Y, Gao Y, Holloway MK, Wang R. Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. J Chem Inf Model 2020; 60:4359-4375. [DOI: 10.1021/acs.jcim.9b00619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
| | - Yingduo Gao
- Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
- Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | | | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- Shanxi Key Laboratory of Innovative Drugs for the Treatment of Serious Diseases Basing on Chronic Inflammation, College of Traditional Chinese Medicines, Shanxi University of Chinese Medicine, Taiyuan, Shanxi 030619, People’s Republic of China
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3
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Goel H, Yu W, Ustach VD, Aytenfisu AH, Sun D, MacKerell AD. Impact of electronic polarizability on protein-functional group interactions. Phys Chem Chem Phys 2020; 22:6848-6860. [PMID: 32195493 PMCID: PMC7194236 DOI: 10.1039/d0cp00088d] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Interactions of proteins with functional groups are key to their biological functions, making it essential that they be accurately modeled. To investigate the impact of the inclusion of explicit treatment of electronic polarizability in force fields on protein-functional group interactions, the additive CHARMM and Drude polarizable force field are compared in the context of the Site-Identification by Ligand Competitive Saturation (SILCS) simulation methodology from which functional group interaction patterns with five proteins for which experimental binding affinities of multiple ligands are available, were obtained. The explicit treatment of polarizability produces significant differences in the functional group interactions in the ligand binding sites including overall enhanced binding of functional groups to the proteins. This is associated with variations of the dipole moments of solutes representative of functional groups in the binding sites relative to aqueous solution with higher dipole moments systematically occurring in the latter, though exceptions occur with positively charged methylammonium. Such variation indicates the complex, heterogeneous nature of the electronic environments of ligand binding sites and emphasizes the inherent limitation of fixed charged, additive force fields for modeling ligand-protein interactions. These effects yield more defined orientation of the functional groups in the binding pockets and a small, but systematic improvement in the ability of the SILCS method to predict the binding orientation and relative affinities of ligands to their target proteins. Overall, these results indicate that the physical model associated with the explicit treatment of polarizability along with the presence of lone pairs in a force field leads to changes in the nature of the interactions of functional groups with proteins versus that occurring with additive force fields, suggesting the utility of polarizable force fields in obtaining a more realistic understanding of protein-ligand interactions.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Vincent D Ustach
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Asaminew H Aytenfisu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Delin Sun
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St., Baltimore, Maryland 21201, USA.
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4
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Wang S, Cai SL, Zhang J, Wan XH. Tunable Cis-cisoid Helical Conformation of Poly(3,5-disubstibuted phenylacetylene)s Stabilized by n→π* Interaction. CHINESE JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1007/s10118-020-2376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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5
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Hao X, Zuo X, Kang D, Zhang J, Song Y, Liu X, Zhan P. Contemporary medicinal-chemistry strategies for discovery of blood coagulation factor Xa inhibitors. Expert Opin Drug Discov 2019; 14:915-931. [DOI: 10.1080/17460441.2019.1626821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Xiaofang Zuo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, Jinan, China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Ji’nan, Shandong, PR China
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6
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Ngo ST, Vu KB, Bui LM, Vu VV. Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method. ACS OMEGA 2019; 4:3887-3893. [PMID: 31459599 PMCID: PMC6648447 DOI: 10.1021/acsomega.8b03258] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical
and Computational Biophysics, Ton Duc Thang
University, Ho Chi Minh City 7000000, Vietnam
- Faculty
of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 7000000, Vietnam
| | - Khanh B. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Le Minh Bui
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
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7
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Zhu C, Li G, Xiao K, Shao X, Cheng J, Li Z. Water bridges are essential to neonicotinoids: Insights from synthesis, bioassay and molecular modelling studies. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Subramanian V, Ain QU, Henno H, Pietilä LO, Fuchs JE, Prusis P, Bender A, Wohlfahrt G. 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. MEDCHEMCOMM 2017; 8:1037-1045. [PMID: 30108817 PMCID: PMC6072133 DOI: 10.1039/c6md00701e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/14/2017] [Indexed: 11/21/2022]
Abstract
The high similarity between certain sub-pockets of serine proteases may lead to low selectivity of protease inhibitors. Therefore the application of proteochemometrics (PCM), which quantifies the relationship between protein/ligand descriptors and affinity for multiple ligands and targets simultaneously, is useful to understand and improve the selectivity profiles of potential inhibitors. In this study, protein field-based PCM that uses knowledge-based and WaterMap derived fields to describe proteins in combination with 2D (RDKit and MOE fingerprints) and 3D (4 point pharmacophoric fingerprints and GRIND) ligand descriptors was used to model the bioactivities of 24 homologous serine proteases and 5863 inhibitors in an integrated fashion. Of the multiple field-based PCM models generated based on different ligand descriptors, RDKit fingerprints showed the best performance in terms of external prediction with Rtest2 of 0.72 and RMSEP of 0.81. Further, visual interpretation of the models highlights sub-pocket specific regions that influence affinity and selectivity of serine protease inhibitors.
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Affiliation(s)
- Vigneshwari Subramanian
- Division of Pharmaceutical Chemistry and Technology , Faculty of Pharmacy , University of Helsinki , 00014 Helsinki , Finland
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Qurrat Ul Ain
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
| | - Helena Henno
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Lars-Olof Pietilä
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Julian E Fuchs
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
- Institute of General , Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 82 , 6020 Innsbruck , Austria
| | - Peteris Prusis
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Andreas Bender
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
| | - Gerd Wohlfahrt
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
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9
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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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: 40] [Impact Index Per Article: 5.0] [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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11
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Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. J Phys Chem B 2016; 120:8743-56. [PMID: 27169482 DOI: 10.1021/acs.jpcb.6b01094] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.
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Affiliation(s)
- Kamran Haider
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States
| | - Lauren Wickstrom
- Borough of Manhattan Community College, Department of Science, The City University of New York , 199 Chambers Street, New York, New York 10007, United States
| | - Steven Ramsey
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Biochemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
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12
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Theoretical Study of Molecular Structure and Physicochemical Properties of Novel Factor Xa Inhibitors and Dual Factor Xa and Factor IIa Inhibitors. Molecules 2016; 21:molecules21020185. [PMID: 26861270 PMCID: PMC6273828 DOI: 10.3390/molecules21020185] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 12/13/2022] Open
Abstract
The geometries and energies of factor Xa inhibitors edoxaban, eribaxaban, fidexaban, darexaban, letaxaban, and the dual factor Xa and thrombin inhibitors tanogitran and SAR107375 in both the gas-phase and aqueous solution were studied using the Becke3LYP/6-31++G(d,p) or Grimme’s B97D/6-31++G(d,p) method. The fully optimized conformers of these anticoagulants show a characteristic l-shape structure, and the water had a remarkable effect on the equilibrium geometry. According to the calculated pKa values eribaxaban and letaxaban are in neutral undissociated form at pH 7.4, while fidexaban and tanogitran exist as zwitterionic structures. The lipophilicity of the inhibitors studied lies within a large range of log P between 1 and 4. The dual inhibitor SAR107375 represents an improvement in structural, physicochemical and pharmacokinetic characteristics over tanogitran. At blood pH, SAR107375 predominantly exists in neutral form. In contrast with tanogitran, it is better absorbed and more lipophilic and active after oral application.
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13
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Nguyen CN, Kurtzman T, Gilson MK. Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. J Chem Theory Comput 2015; 12:414-29. [PMID: 26636620 PMCID: PMC4819442 DOI: 10.1021/acs.jctc.5b00939] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A number
of computational tools available today compute the thermodynamic properties
of water at surfaces and in binding pockets by using inhomogeneous
solvation theory (IST) to analyze explicit-solvent simulations. Such
methods enable qualitative spatial mappings of both energy and entropy
around a solute of interest and can also be applied quantitatively.
However, the entropy estimates of existing methods have, to date,
been almost entirely limited to the first-order terms in the IST’s
entropy expansion. These first-order terms account for localization
and orientation of water molecules in the field of the solute but
not for the modification of water–water correlations by the
solute. Here, we present an extension of the Grid Inhomogeneous Solvation
Theory (GIST) approach which accounts for water–water translational
correlations. The method involves rewriting the two-point density
of water in terms of a conditional density and utilizes the efficient
nearest-neighbor entropy estimation approach. Spatial maps of this
second order term, for water in and around the synthetic host cucurbit[7]uril
and in the binding pocket of the enzyme Factor Xa, reveal mainly negative
contributions, indicating solute-induced water–water correlations
relative to bulk water; particularly strong signals are obtained for
sites at the entrances of cavities or pockets. This second-order term
thus enters with the same, negative, sign as the first order translational
and orientational terms. Numerical and convergence properties of the
methodology are examined.
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Affiliation(s)
- Crystal N Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Blvd. West, Bronx, New York, New York 10468, United States.,Ph.D. Program in Chemistry, The Graduate Center of The City University of New York , New York 10016, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
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14
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Raman EP, MacKerell AD. Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability. J Am Chem Soc 2015; 137:2608-21. [PMID: 25625202 DOI: 10.1021/ja512054f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The thermodynamic driving forces behind small molecule-protein binding are still not well-understood, including the variability of those forces associated with different types of ligands in different binding pockets. To better understand these phenomena we calculate spatially resolved thermodynamic contributions of the different molecular degrees of freedom for the binding of propane and methanol to multiple pockets on the proteins Factor Xa and p38 MAP kinase. Binding thermodynamics are computed using a statistical thermodynamics based end-point method applied on a canonical ensemble comprising the protein-ligand complexes and the corresponding free states in an explicit solvent environment. Energetic and entropic contributions of water and ligand degrees of freedom computed from the configurational ensemble provide an unprecedented level of detail into the mechanisms of binding. Direct protein-ligand interaction energies play a significant role in both nonpolar and polar binding, which is comparable to water reorganization energy. Loss of interactions with water upon binding strongly compensates these contributions leading to relatively small binding enthalpies. For both solutes, the entropy of water reorganization is found to favor binding in agreement with the classical view of the "hydrophobic effect". Depending on the specifics of the binding pocket, both energy-entropy compensation and reinforcement mechanisms are observed. It is notable to have the ability to visualize the spatial distribution of the thermodynamic contributions to binding at atomic resolution showing significant differences in the thermodynamic contributions of water to the binding of propane versus methanol.
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Affiliation(s)
- E Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 Penn Street HSF II, Baltimore, Maryland 21201, United States
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15
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Yu W, Lakkaraju SK, Raman EP, Fang L, MacKerell AD. Pharmacophore modeling using site-identification by ligand competitive saturation (SILCS) with multiple probe molecules. J Chem Inf Model 2015; 55:407-20. [PMID: 25622696 DOI: 10.1021/ci500691p] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Receptor-based pharmacophore modeling is an efficient computer-aided drug design technique that uses the structure of the target protein to identify novel leads. However, most methods consider protein flexibility and desolvation effects in a very approximate way, which may limit their use in practice. The Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling protocol (SILCS-Pharm) was introduced recently to address these issues, as SILCS naturally takes both protein flexibility and desolvation effects into account by using full molecular dynamics simulations to determine 3D maps of the functional group-affinity patterns on a target receptor. In the present work, the SILCS-Pharm protocol is extended to use a wider range of probe molecules including benzene, propane, methanol, formamide, acetaldehyde, methylammonium, acetate and water. This approach removes the previous ambiguity brought by using water as both the hydrogen-bond donor and acceptor probe molecule. The new SILCS-Pharm protocol is shown to yield improved screening results, as compared to the previous approach based on three target proteins. Further validation of the new protocol using five additional protein targets showed improved screening compared to those using common docking methods, further indicating improvements brought by the explicit inclusion of additional feature types associated with the wider collection of probe molecules in the SILCS simulations. The advantage of using complementary features and volume constraints, based on exclusion maps of the protein defined from the SILCS simulations, is presented. In addition, reranking using SILCS-based ligand grid free energies is shown to enhance the diversity of identified ligands for the majority of targets. These results suggest that the SILCS-Pharm protocol will be of utility in rational drug design.
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Affiliation(s)
- Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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16
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Gerogiokas G, Southey MWY, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J. Evaluation of water displacement energetics in protein binding sites with grid cell theory. Phys Chem Chem Phys 2015; 17:8416-26. [DOI: 10.1039/c4cp05572a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The grid cell theory method was used to elucidate perturbations in water network energetics in a range of protein–ligand complexes.
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Affiliation(s)
| | | | | | | | | | | | - J. Michel
- EaStCHEM School of Chemistry
- Edinburgh
- UK
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17
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Promising coagulation factor VIII bypassing strategies for patients with haemophilia A. Blood Coagul Fibrinolysis 2014; 25:539-52. [DOI: 10.1097/mbc.0000000000000098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. J Chem Theory Comput 2014; 10:2769-2780. [PMID: 25018673 PMCID: PMC4089914 DOI: 10.1021/ct401110x] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 01/04/2023]
Abstract
Water molecules in the active site of an enzyme occupy a complex, heterogeneous environment, and the thermodynamic properties of active-site water are functions of position. As a consequence, it is thought that an enzyme inhibitor can gain affinity by extending into a region occupied by unfavorable water or lose affinity by displacing water from a region where it was relatively stable. Recent advances in the characterization of binding-site water, based on the analysis of molecular simulations with explicit water molecules, have focused largely on simplified representations of water as occupying well-defined hydration sites. Our grid-based treatment of hydration, GIST, offers a more complete picture of the complex distributions of water properties, but it has not yet been applied to proteins. This first application of GIST to protein-ligand modeling, for the case of Coagulation Factor Xa, shows that ligand scoring functions based on GIST perform at least as well as scoring functions based on a hydration-site approach (HSA), when applied to exactly the same simulation data. Interestingly, the displacement of energetically unfavorable water emerges as the dominant factor in the fitted scoring functions, for both GIST and HSA methods, while water entropy plays a secondary role, at least in the present context.
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Affiliation(s)
- Crystal N Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Anthony Cruz
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Blvd. West, Bronx, New York 10468, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Blvd. West, Bronx, New York 10468, United States
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19
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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20
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Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Automating crystallographic structure solution and refinement of protein-ligand complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:144-54. [PMID: 24419387 PMCID: PMC3919266 DOI: 10.1107/s139900471302748x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
Abstract
High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation.
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Affiliation(s)
- Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Herbert E. Klei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Jeffrey J. Headd
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | | | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720-1762, USA
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21
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Raman EP, Yu W, Lakkaraju SK, MacKerell AD. Inclusion of multiple fragment types in the site identification by ligand competitive saturation (SILCS) approach. J Chem Inf Model 2013; 53:3384-98. [PMID: 24245913 DOI: 10.1021/ci4005628] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The site identification by ligand competitive saturation (SILCS) method identifies the location and approximate affinities of small molecular fragments on a target macromolecular surface by performing molecular dynamics (MD) simulations of the target in an aqueous solution of small molecules representative of different chemical functional groups. In this study, we introduce a set of small molecules to map potential interactions made by neutral hydrogen bond donors and acceptors and charged donor and acceptor fragments in addition to nonpolar fragments. The affinity pattern is obtained in the form of discretized probability or, equivalently, free energy maps, called FragMaps, which can be visualized with the target surface. We performed SILCS simulations for four proteins for which structural and thermodynamic data is available for multiple diverse ligands. Good overlap is shown between high affinity regions identified by the FragMaps and the crystallographic positions of ligand functional groups with similar chemical functionality, thus demonstrating the validity of the qualitative information obtained from the simulations. To test the ability of FragMaps in providing quantitative predictions, we calculate the previously introduced ligand grid free energy (LGFE) metric and observe its correspondence with experimentally measured binding affinity. LGFE is computed for different conformational ensembles and improvement in prediction is shown with increasing ligand conformational sampling. Ensemble generation includes a Monte Carlo sampling approach that uses the GFE FragMaps directly as the energy function. The results show that some but not all experimental trends are predicted and warrant improvements in the scoring methodology. In addition, the potential utility of atom-based free energy contributions to the LGFE scores and the use of multiple ligands in SILCS to identify displaceable water molecules during ligand design are discussed.
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Affiliation(s)
- E Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , 20 Penn Street HSF II, Baltimore, Maryland 21201 United States
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22
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Kamer KJ, Choudhary A, Raines RT. Intimate interactions with carbonyl groups: dipole-dipole or n→π*? J Org Chem 2013; 78:2099-103. [PMID: 23163960 PMCID: PMC3586291 DOI: 10.1021/jo302265k] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amide carbonyl groups in proteins can engage in C═O···C═O and C-X···C═O interactions, where X is a halogen. The putative involvement of four poles suggests that these interactions are primarily dipolar. Our survey of crystal structures with a C-X···C═O contact that is short (i.e., within the sum of the X and C van der Waals radii) revealed no preferred C-X···C═O dihedral angle. Moreover, we found that structures with a short X(-)···C═O contact display the signatures of an n→π* interaction. We conclude that intimate interactions with carbonyl groups do not require a dipole.
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Affiliation(s)
- Kimberli J. Kamer
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Amit Choudhary
- Graduate Program in Biophysics, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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23
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Genheden S. Are homology models sufficiently good for free-energy simulations? J Chem Inf Model 2012; 52:3013-21. [PMID: 23113602 DOI: 10.1021/ci300349s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this paper, I evaluate the usefulness of protein homology models in rigorous free-energy simulations to determine ligand affinities. Two templates were used to create models of the factor Xa protein and one template was used for dihydrofolate reductase from Plasmodium falciparum. Then, the relative free energies for several pairs of ligands were estimated using thermodynamic integration with the homology models as starting point of the simulation. These binding affinities were compared to affinities obtained when using published crystal structures as starting point of the simulations. Encouragingly, the differences between the affinities obtained when starting from either homology models or crystal structure were not statistical significant for a majority of the considered pairs of ligands. Differences between 1 and 2 kJ/mol were observed for the dihydrofolate reductase ligands and differences between 0 and 8 kJ/mol were observed for the factor Xa ligands. The largest difference for factor Xa was caused by an erroneous modeling of a loop region close to two of the ligands, and it was only observed when using one of the templates. Therefore, it is advisible to always use more than one template when creating homology models if they should be used in free-energy simulations.
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Affiliation(s)
- Samuel Genheden
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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24
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Chandrasekaran M, Sakkiah S, Lee KW. Combined chemical feature-based assessment and Bayesian model studies to identify potential inhibitors for Factor Xa. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9936-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Huggins DJ, Tidor B. Systematic placement of structural water molecules for improved scoring of protein-ligand interactions. Protein Eng Des Sel 2011; 24:777-89. [PMID: 21771870 PMCID: PMC3170077 DOI: 10.1093/protein/gzr036] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 06/03/2011] [Accepted: 06/15/2011] [Indexed: 11/13/2022] Open
Abstract
Structural water molecules are found in many protein-ligand complexes. They are known to be vital in mediating hydrogen-bonding interactions and, in some cases, key for facilitating tight binding. It is thus very important to consider water molecules when attempting to model protein-ligand interactions for cognate ligand identification, virtual screening and drug design. While the rigid treatment of water molecules present in structures is feasible, the more relevant task of treating all possible positions and orientations of water molecules with each possible ligand pose is computationally daunting. Current methods in molecular docking provide partial treatment for such water molecules, with modest success. Here we describe a new method employing dead-end elimination to place water molecules within a binding site, bridging interactions between protein and ligand. Dead-end elimination permits a thorough, though still incomplete, treatment of water placement. The results show that this method is able to place water molecules correctly within known complexes and to create physically reasonable hydrogen bonds. The approach has also been incorporated within an inverse molecular design approach, to model a variety of compounds in the process of de novo ligand design. The inclusion of structural water molecules, combined with ranking based on the electrostatic contribution to binding affinity, improves a number of otherwise poor energetic predictions.
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Affiliation(s)
- David J. Huggins
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139–4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139–4307, USA
| | - Bruce Tidor
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139–4307, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139–4307, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139–4307, USA
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26
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Bhunia SS, Roy KK, Saxena AK. Profiling the structural determinants for the selectivity of representative factor-Xa and thrombin inhibitors using combined ligand-based and structure-based approaches. J Chem Inf Model 2011; 51:1966-85. [PMID: 21761917 DOI: 10.1021/ci200185q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The current study deciphers the combined ligand- and structure-based computational insights to profile structural determinants for the selectivity of representative diverse classes of FXa-selective and thrombin-selective as well as dual FXa-thrombin high affinity inhibitors. The thrombin-exclusive insertion 60-loop (D-pocket) was observed to be one of the most notable recognition sites for the known thrombin-selective inhibitors. Based on the topological comparison of four common active-site pockets (S1-S4) of FXa and thrombin, the greater structural disparity was observed in the S4-pocket, which was more symmetrical (U-shaped) in FXa as compared to thrombin mainly due to the presence of L99 and I174 residues in latter in place of Y99 and F174 respectively in former protease. The S2 pocket forming partial roof at the entry of 12 Å deep S1-pocket, with two extended β-sheets running antiparallel to each other by undergoing U-turn (∼180̊), has two conserved glycine residues forming H-bonds with the bound ligand for governing ligand binding affinity. The docking, scoring, and binding pose comparison of the representative high-affinity and selective inhibitors into the active sites of FXa and thrombin revealed critical residues (S214, Y99, W60D) mediating selectivity through direct- and long-range electrostatic interactions. Interestingly, most of the thrombin-selective inhibitors attained S-shaped conformation in thrombin, while FXa-selective inhibitors attained L-shaped conformations in FXa. The role of residue at 99th position of FXa and thrombin toward governing protease selectivity was further substantiated using molecular dynamics simulations on the wild-type and mutated Y99L FXa bound to thrombin-selective inhibitor 2. Furthermore, predictive CoMFA (FXa q² = 0.814; thrombin q² = 0.667) and CoMSIA (FXa q² = 0.807; thrombin q² = 0.624) models were developed and validated (FXa r²(test) = 0.823; thrombin r(2)(test) = 0.816) to feature molecular determinants of ligand binding affinity using the docking-based conformational alignments (DBCA) of 141 (88(train)+53(test)) and 39 (27(train)+11(test)) nonamidine class of potent FXa (0.004 ≤ K(i) (nM) ≤ 4700) and thrombin (0.001 ≤ K(i) (nM) ≤ 940) inhibitors, respectively. Interestingly, the ligand-based insights well corroborated with the structure-based insights in terms of the role of steric, electrostatic, and hydrophobic parameters for governing the selectivity for the two proteases. The new computational insights presented in this study are expected to be valuable for understanding and designing potent and selective antithrombotic agents.
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Affiliation(s)
- Shome S Bhunia
- Division of Medicinal and Process Chemistry, Central Drug Research Institute, CSIR, Lucknow, India
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27
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Su YC, Miller TN, Navaneetham D, Schoonmaker RT, Sinha D, Walsh PN. The role of factor XIa (FXIa) catalytic domain exosite residues in substrate catalysis and inhibition by the Kunitz protease inhibitor domain of protease nexin 2. J Biol Chem 2011; 286:31904-14. [PMID: 21778227 DOI: 10.1074/jbc.m111.257527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To select residues in coagulation factor XIa (FXIa) potentially important for substrate and inhibitor interactions, we examined the crystal structure of the complex between the catalytic domain of FXIa and the Kunitz protease inhibitor (KPI) domain of a physiologically relevant FXIa inhibitor, protease nexin 2 (PN2). Six FXIa catalytic domain residues (Glu(98), Tyr(143), Ile(151), Arg(3704), Lys(192), and Tyr(5901)) were subjected to mutational analysis to investigate the molecular interactions between FXIa and the small synthetic substrate (S-2366), the macromolecular substrate (factor IX (FIX)) and inhibitor PN2KPI. Analysis of all six Ala mutants demonstrated normal K(m) values for S-2366 hydrolysis, indicating normal substrate binding compared with plasma FXIa; however, all except E98A and K192A had impaired values of k(cat) for S-2366 hydrolysis. All six Ala mutants displayed deficient k(cat) values for FIX hydrolysis, and all were inhibited by PN2KPI with normal values of K(i) except for K192A, and Y5901A, which displayed increased values of K(i). The integrity of the S1 binding site residue, Asp(189), utilizing p-aminobenzamidine, was intact for all FXIa mutants. Thus, whereas all six residues are essential for catalysis of the macromolecular substrate (FIX), only four (Tyr(143), Ile(151), Arg(3704), and Tyr(5901)) are important for S-2366 hydrolysis; Glu(98) and Lys(192) are essential for FIX but not S-2366 hydrolysis; and Lys(192) and Tyr(5901) are required for both inhibitor and macromolecular substrate interactions.
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Affiliation(s)
- Ya-Chi Su
- Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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28
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Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. ChemMedChem 2011; 6:1049-66. [PMID: 21506273 DOI: 10.1002/cmdc.201000533] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/08/2011] [Indexed: 11/12/2022]
Abstract
The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.
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29
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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30
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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31
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Pharmacophore alignment search tool: Influence of the third dimension on text-based similarity searching. J Comput Chem 2011; 32:1618-34. [DOI: 10.1002/jcc.21742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 11/07/2022]
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32
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Lee YK, Player MR. Developments in factor Xa inhibitors for the treatment of thromboembolic disorders. Med Res Rev 2011; 31:202-83. [DOI: 10.1002/med.20183] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Fujimoto T, Imaeda Y, Konishi N, Hiroe K, Kawamura M, Textor GP, Aertgeerts K, Kubo K. Discovery of a tetrahydropyrimidin-2(1H)-one derivative (TAK-442) as a potent, selective, and orally active factor Xa inhibitor. J Med Chem 2010; 53:3517-31. [PMID: 20355714 DOI: 10.1021/jm901699j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coagulation enzyme factor Xa (FXa) is a particularly promising target for the development of new anticoagulant agents. We previously reported the imidazo[1,5-c]imidazol-3-one derivative 1 as a potent and orally active FXa inhibitor. However, it was found that 1 predominantly undergoes hydrolysis upon incubation with human liver microsomes, and the human specific metabolic pathway made it difficult to predict the human pharmacokinetics. To address this issue, our synthetic efforts were focused on modification of the imidazo[1,5-c]imidazol-3-one moiety of the active metabolite 3a, derived from 1, which resulted in the discovery of the tetrahydropyrimidin-2(1H)-one derivative 5k as a highly potent and selective FXa inhibitor. Compound 5k showed no detectable amide bond cleavage in human liver microsomes, exhibited a good pharmacokinetic profile in monkeys, and had a potent antithrombotic efficacy in a rabbit model without prolongation of bleeding time. Compound 5k is currently under clinical development with the code name TAK-442.
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Affiliation(s)
- Takuya Fujimoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 2-17-85, Jusohomachi, Yodogawa-ku, Osaka 532-8686, Japan
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34
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Fujimura KI, Sasabuchi Y. The Role of Fluorine Atoms in a Fluorinated Prostaglandin Agonist. ChemMedChem 2010; 5:1254-7. [DOI: 10.1002/cmdc.201000174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Abstract
The MEROPS website (http://merops.sanger.ac.uk) includes information on peptidase inhibitors as well as on peptidases and their substrates. Displays have been put in place to link peptidases and inhibitors together. The classification of protein peptidase inhibitors is continually being revised, and currently inhibitors are grouped into 67 families based on comparisons of protein sequences. These families can be further grouped into 38 clans based on comparisons of tertiary structure. Small molecule inhibitors are important reagents for peptidase characterization and, with the increasing importance of peptidases as drug targets, they are also important to the pharmaceutical industry. Small molecule inhibitors are now included in MEROPS and over 160 summaries have been written.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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36
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Buddai SK, Layzer JM, Lu G, Rusconi CP, Sullenger BA, Monroe DM, Krishnaswamy S. An anticoagulant RNA aptamer that inhibits proteinase-cofactor interactions within prothrombinase. J Biol Chem 2009; 285:5212-23. [PMID: 20022942 DOI: 10.1074/jbc.m109.049833] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of factor Xa with factor Va on membranes to form prothrombinase profoundly increases the rate of the proteolytic conversion of prothrombin to thrombin. We present the characterization of an RNA aptamer (RNA(11F7t)) selected from a combinatorial library based on its ability to bind factor Xa. We show that RNA(11F7t) inhibits thrombin formation catalyzed by prothrombinase without obscuring the active site of Xa within the enzyme complex. Selective inhibition of protein substrate cleavage arises from the ability of the aptamer to bind to factor Xa and exclude interactions between the proteinase and cofactor within prothrombinase. Competition for enzyme complex assembly results from the binding of RNA(11F7t) to factor Xa with nanomolar affinity in a Ca(2+)-dependent interaction. RNA(11F7t) binds equivalently to the zymogen factor X as well as derivatives lacking gamma-carboxyglutamic acid residues. We suggest that the ability of RNA(11F7t) to compete for the Xa-Va interaction with surprisingly high affinity likely reflects a significant contribution from its ability to indirectly impact regions of Xa that participate in the proteinase-cofactor interaction. Thus, despite the complexity of the macromolecular interactions that underlie the assembly of prothrombinase, efficient inhibition of enzyme complex assembly and thrombin formation can be achieved by tight binding ligands that target factor Xa in a discrete manner.
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Affiliation(s)
- Sai K Buddai
- Joseph Stokes Research Institute, Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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37
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Zögg T, Brandstetter H. Structural Basis of the Cofactor- and Substrate-Assisted Activation of Human Coagulation Factor IXa. Structure 2009; 17:1669-1678. [DOI: 10.1016/j.str.2009.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 10/05/2009] [Accepted: 10/07/2009] [Indexed: 10/20/2022]
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38
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Vagenende V, Yap MGS, Trout BL. Molecular Anatomy of Preferential Interaction Coefficients by Elucidating Protein Solvation in Mixed Solvents: Methodology and Application for Lysozyme in Aqueous Glycerol. J Phys Chem B 2009; 113:11743-53. [DOI: 10.1021/jp903413v] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Vincent Vagenende
- Singapore−MIT Alliance, National University of Singapore, 4 Engineering Drive 3, Singapore 117576, Bioprocessing Technology Institute, 20 Biopolis Way #06-01 Centros, Singapore 138668, and Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Miranda G. S. Yap
- Singapore−MIT Alliance, National University of Singapore, 4 Engineering Drive 3, Singapore 117576, Bioprocessing Technology Institute, 20 Biopolis Way #06-01 Centros, Singapore 138668, and Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
| | - Bernhardt L. Trout
- Singapore−MIT Alliance, National University of Singapore, 4 Engineering Drive 3, Singapore 117576, Bioprocessing Technology Institute, 20 Biopolis Way #06-01 Centros, Singapore 138668, and Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139
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39
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Li X, He X, Wang B, Merz K. Conformational variability of benzamidinium-based inhibitors. J Am Chem Soc 2009; 131:7742-54. [PMID: 19435349 DOI: 10.1021/ja9010833] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determining the structure of a small molecule bound to a biological receptor (e.g., a protein implicated in a disease state) is a necessary step in structure-based drug design. The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule for its receptor. However, the quality of a protein/ligand complex determined using X-ray crystallography is dependent on the size of the protein, the crystal quality, and the realized resolution. The energy restraints used in traditional X-ray refinement procedures typically use "reduced" (i.e., neglect of electrostatics and dispersion interactions) Engh and Huber force field models that, while quite suitable for modeling proteins, often are less suitable for small molecule structures due to a lack of validated parameters. Through the use of ab initio QM/MM-based X-ray refinement procedures, this shortcoming can be overcome especially in the active site or binding site of a small-molecule inhibitor. Herein, we demonstrate that ab initio QM/MM refinement of an inhibitor/protein complex provides insights into the binding of small molecules beyond what is available using more traditional refinement protocols. In particular, QM/MM refinement studies of benzamidinium derivatives show variable conformational preferences depending on the refinement protocol used and the nature of the active-site region.
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Affiliation(s)
- Xue Li
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA
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40
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Tanrikulu Y, Proschak E, Werner T, Geppert T, Todoroff N, Klenner A, Kottke T, Sander K, Schneider E, Seifert R, Stark H, Clark T, Schneider G. Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H4Receptor. ChemMedChem 2009; 4:820-7. [DOI: 10.1002/cmdc.200800443] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Shi Y, Sitkoff D, Zhang J, Klei HE, Kish K, Liu ECK, Hartl KS, Seiler SM, Chang M, Huang C, Youssef S, Steinbacher TE, Schumacher WA, Grazier N, Pudzianowski A, Apedo A, Discenza L, Yanchunas J, Stein PD, Atwal KS. Design, structure-activity relationships, X-ray crystal structure, and energetic contributions of a critical P1 pharmacophore: 3-chloroindole-7-yl-based factor Xa inhibitors. J Med Chem 2009; 51:7541-51. [PMID: 18998662 DOI: 10.1021/jm800855x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An indole-based P1 moiety was incorporated into a previously established factor Xa inhibitor series. The indole group was designed to hydrogen-bond with the carbonyl of Gly218, while its 3-methyl or 3-chloro substituent was intended to interact with Tyr228. These interactions were subsequently observed in the X-ray crystal structure of compound 18. SAR studies led to the identification of compound 20 as the most potent FXa inhibitor in this series (IC(50) = 2.4 nM, EC(2xPT) = 1.2 microM). An in-depth energetic analysis suggests that the increased binding energy of 3-chloroindole-versus 3-methylindole-containing compounds in this series is due primarily to (a) the more hydrophobic nature of chloro- versus methyl-containing compounds and (b) an increased interaction of 3-chloroindole versus 3-methylindole with Gly218 backbone. The stronger hydrophobicity of chloro- versus methyl-substituted aromatics may partly explain the general preference for chloro- versus methyl-substituted P1 groups in FXa, which extends beyond the current series.
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Affiliation(s)
- Yan Shi
- Bristol-Myers Squibb Research & Development, P.O. Box 5400, Princeton, New Jersey 08543-5400, USA.
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42
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de Candia M, Liantonio F, Carotti A, De Cristofaro R, Altomare C. Fluorinated Benzyloxyphenyl Piperidine-4-carboxamides with Dual Function against Thrombosis: Inhibitors of Factor Xa and Platelet Aggregation. J Med Chem 2009; 52:1018-28. [DOI: 10.1021/jm801141f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Modesto de Candia
- Dipartimento Farmaco-chimico, University of Bari, Via Orabona 4, I-70125, Bari, Italy, Hemostasis Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Largo F. Vito 1, I-00168 Rome, Italy
| | - Francesco Liantonio
- Dipartimento Farmaco-chimico, University of Bari, Via Orabona 4, I-70125, Bari, Italy, Hemostasis Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Largo F. Vito 1, I-00168 Rome, Italy
| | - Andrea Carotti
- Dipartimento Farmaco-chimico, University of Bari, Via Orabona 4, I-70125, Bari, Italy, Hemostasis Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Largo F. Vito 1, I-00168 Rome, Italy
| | - Raimondo De Cristofaro
- Dipartimento Farmaco-chimico, University of Bari, Via Orabona 4, I-70125, Bari, Italy, Hemostasis Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Largo F. Vito 1, I-00168 Rome, Italy
| | - Cosimo Altomare
- Dipartimento Farmaco-chimico, University of Bari, Via Orabona 4, I-70125, Bari, Italy, Hemostasis Research Centre, Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Largo F. Vito 1, I-00168 Rome, Italy
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43
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Singh N, Briggs JM. Molecular dynamics simulations of Factor Xa: insight into conformational transition of its binding subsites. Biopolymers 2008; 89:1104-13. [PMID: 18680100 DOI: 10.1002/bip.21062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein flexibility and conformational diversity is well known to be a key characteristic of the function of many proteins. Human blood coagulation proteins have multiple substrates, and various protein-protein interactions are required for the smooth functioning of the coagulation cascade to maintain blood hemostasis. To address how a protein may cope with multiple interactions with its structurally diverse substrates and the accompanied structural changes that may drive these changes, we studied human Factor X. We employed 20 ns of molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on two different conformational forms of Factor X, open and closed, and observed an interchangeable conformational transition from one to another. This work also demonstrates the roles of various aromatic residues involved in aromatic-aromatic interactions, which make this dynamic transition possible.
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Affiliation(s)
- Narender Singh
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204-5001, USA
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44
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Achieving structural diversity using the perpendicular conformation of alpha-substituted phenylcyclopropanes to mimic the bioactive conformation of ortho-substituted biphenyl P4 moieties: Discovery of novel, highly potent inhibitors of Factor Xa. Bioorg Med Chem Lett 2008; 18:4118-23. [DOI: 10.1016/j.bmcl.2008.05.095] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 05/21/2008] [Accepted: 05/22/2008] [Indexed: 11/18/2022]
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45
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Yang L, Manithody C, Rezaie AR. The role of autolysis loop in determining the specificity of coagulation proteases. ACTA ACUST UNITED AC 2008; 40:1055-64. [PMID: 17665041 DOI: 10.1590/s0100-879x2006005000137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/23/2007] [Indexed: 11/21/2022]
Abstract
We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system) of activated protein C (APC) with the corresponding loop of factor Xa (fXa) renders the APC mutant (APC/fX143-154) susceptible to inhibition by antithrombin (AT) in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154). Unlike an approximately 500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved approximately 10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.
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Affiliation(s)
- L Yang
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, 1402 S. Grand Boulevard, St. Louis, MO 63104, USA
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46
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Abel R, Young T, Farid R, Berne BJ, Friesner RA. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc 2008; 130:2817-31. [PMID: 18266362 PMCID: PMC2761766 DOI: 10.1021/ja0771033] [Citation(s) in RCA: 514] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the underlying physics of the binding of small-molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying molecular physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small molecule and its associated receptor that captures the effects of the ligand displacing the solvent from the protein active site with atomic detail. This descriptor quantitatively predicts (R(2) = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates physical properties of the active-site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.
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Affiliation(s)
- Robert Abel
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Tom Young
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Ramy Farid
- Schrödinger, Inc, 120 West 45th Street, New York, New York 10036
| | - Bruce J. Berne
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Richard A. Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
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47
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Macedo-Ribeiro S, Almeida C, Calisto BM, Friedrich T, Mentele R, Stürzebecher J, Fuentes-Prior P, Pereira PJB. Isolation, cloning and structural characterisation of boophilin, a multifunctional Kunitz-type proteinase inhibitor from the cattle tick. PLoS One 2008; 3:e1624. [PMID: 18286181 PMCID: PMC2230226 DOI: 10.1371/journal.pone.0001624] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2007] [Accepted: 01/20/2008] [Indexed: 11/19/2022] Open
Abstract
Inhibitors of coagulation factors from blood-feeding animals display a wide variety of structural motifs and inhibition mechanisms. We have isolated a novel inhibitor from the cattle tick Boophilus microplus, one of the most widespread parasites of farm animals. The inhibitor, which we have termed boophilin, has been cloned and overexpressed in Escherichia coli. Mature boophilin is composed of two canonical Kunitz-type domains, and inhibits not only the major procoagulant enzyme, thrombin, but in addition, and by contrast to all other previously characterised natural thrombin inhibitors, significantly interferes with the proteolytic activity of other serine proteinases such as trypsin and plasmin. The crystal structure of the bovine α-thrombin·boophilin complex, refined at 2.35 Å resolution reveals a non-canonical binding mode to the proteinase. The N-terminal region of the mature inhibitor, Q16-R17-N18, binds in a parallel manner across the active site of the proteinase, with the guanidinium group of R17 anchored in the S1 pocket, while the C-terminal Kunitz domain is negatively charged and docks into the basic exosite I of thrombin. This binding mode resembles the previously characterised thrombin inhibitor, ornithodorin which, unlike boophilin, is composed of two distorted Kunitz modules. Unexpectedly, both boophilin domains adopt markedly different orientations when compared to those of ornithodorin, in its complex with thrombin. The N-terminal boophilin domain rotates 9° and is displaced by 6 Å, while the C-terminal domain rotates almost 6° accompanied by a 3 Å displacement. The reactive-site loop of the N-terminal Kunitz domain of boophilin with its P1 residue, K31, is fully solvent exposed and could thus bind a second trypsin-like proteinase without sterical restraints. This finding explains the formation of a ternary thrombin·boophilin·trypsin complex, and suggests a mechanism for prothrombinase inhibition in vivo.
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Affiliation(s)
- Sandra Macedo-Ribeiro
- Centro de Neurociências e Biologia Celular (CNC), Coimbra, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | - Carla Almeida
- Centro de Neurociências e Biologia Celular (CNC), Coimbra, Portugal
| | - Bárbara M. Calisto
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
| | | | | | | | - Pablo Fuentes-Prior
- Cardiovascular Research Center, Consejo Superior de Investigaciones Científicas (CSIC)-Institut Català de Ciències Cardiovasculars (ICCC), Barcelona, Spain
- *E-mail: (PF); (PP)
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- *E-mail: (PF); (PP)
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48
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Ye B, Arnaiz DO, Chou YL, Griedel BD, Karanjawala R, Lee W, Morrissey MM, Sacchi KL, Sakata ST, Shaw KJ, Wu SC, Zhao Z, Adler M, Cheeseman S, Dole WP, Ewing J, Fitch R, Lentz D, Liang A, Light D, Morser J, Post J, Rumennik G, Subramanyam B, Sullivan ME, Vergona R, Walters J, Wang YX, White KA, Whitlow M, Kochanny MJ. Thiophene-anthranilamides as highly potent and orally available factor Xa inhibitors. J Med Chem 2007; 50:2967-80. [PMID: 17536795 DOI: 10.1021/jm070125f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There remains a high unmet medical need for a safe oral therapy for thrombotic disorders. The serine protease factor Xa (fXa), with its central role in the coagulation cascade, is among the more promising targets for anticoagulant therapy and has been the subject of intensive drug discovery efforts. Investigation of a hit from high-throughput screening identified a series of thiophene-substituted anthranilamides as potent nonamidine fXa inhibitors. Lead optimization by incorporation of hydrophilic groups led to the discovery of compounds with picomolar inhibitory potency and micromolar in vitro anticoagulant activity. Based on their high potency, selectivity, oral pharmacokinetics, and efficacy in a rat venous stasis model of thrombosis, compounds ZK 814048 (10b), ZK 810388 (13a), and ZK 813039 (17m) were advanced into development.
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Affiliation(s)
- Bin Ye
- Berlex Biosciences, Post Office Box 4099, Richmond, California 94804-0099, USA.
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49
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Proschak E, Rupp M, Derksen S, Schneider G. Shapelets: Possibilities and limitations of shape-based virtual screening. J Comput Chem 2007; 29:108-14. [PMID: 17516427 DOI: 10.1002/jcc.20770] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Complementarity of molecular surfaces is crucial for molecular recognition. A method for representation of molecular shape is presented. We decompose the molecular surface into commensurate patches with defined shape by fitting hyperbolical paraboloids onto a triangulated isosurface of the Gaussian model of a molecule. As a result of this decomposition we obtain a 3D graph representation of the molecular shape, which can be used for complete and partial shape matching and isosteric group searching. To point out the possibilities and limitations of shape-only models, we challenged our method by three scenarios in a virtual screening contest: rigid body alignment, consensus shape filtering, and target-specific screening.
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Affiliation(s)
- Ewgenij Proschak
- Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D-60323, Frankfurt am Main, Germany
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50
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Noguchi T, Tanaka N, Nishimata T, Goto R, Hayakawa M, Sugidachi A, Ogawa T, Asai F, Fujimoto K. Cinnamylindoline Derivatives: Synthesis and Factor Xa (FXa) Inhibitory Activities. Chem Pharm Bull (Tokyo) 2007; 55:1494-504. [DOI: 10.1248/cpb.55.1494] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Tetsuji Noguchi
- Medicinal Chemistry Research Laboratories II, Daiichi Sankyo Co., Ltd
| | - Naoki Tanaka
- Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd
| | - Toyoki Nishimata
- Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd
| | - Riki Goto
- Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd
| | - Miho Hayakawa
- Medicinal Chemistry Research Laboratories II, Daiichi Sankyo Co., Ltd
| | | | | | - Fumitoshi Asai
- Biological Research Laboratories II, Daiichi Sankyo Co., Ltd
| | - Koichi Fujimoto
- Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd
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