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Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Quantification of Cation–π Interactions in Protein–Ligand Complexes: Crystal‐Structure Analysis of Factor Xa Bound to a Quaternary Ammonium Ion Ligand

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Integrated Modeling Program, Applied Chemical Theory (IMPACT)

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A hierarchical approach to all‐atom protein loop prediction

inferredcites →https://doi.org/10.1006/jmbi.1993.1441openalex-snapshot

Structure of Human Des(1-45) Factor Xa at 2·2 Å Resolution

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Large-scale networks of hydration water molecules around bovine β-trypsin revealed by cryogenic X-ray crystal structure analysis

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GROMACS 3.0: a package for molecular simulation and trajectory analysis

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1-[3-Aminobenzisoxazol-5′-yl]-3-trifluoromethyl-6-[2′-(3-(R)-hydroxy-N-pyrrolidinyl)methyl-[1,1′]-biphen-4-yl]-1,4,5,6-tetrahydropyrazolo-[3,4-c]-pyridin-7-one (BMS-740808) a highly potent, selective, efficacious, and orally bioavailable inhibitor of blood coagulation factor Xa

inferredcites →https://doi.org/10.1016/j.bmcl.2006.04.053openalex-snapshot

Design and synthesis of orally active pyrrolidin-2-one-based factor Xa inhibitors

inferredcites →https://doi.org/10.1016/j.bmcl.2006.08.027openalex-snapshot

Discovery of potent, efficacious, and orally bioavailable inhibitors of blood coagulation factor Xa with neutral P1 moieties

inferredcites →https://doi.org/10.1016/j.bmcl.2006.08.092openalex-snapshot

Arylsulfonamides: A study of the relationship between activity and conformational preferences for a series of factor Xa inhibitors

inferredcites →https://doi.org/10.1016/j.bmcl.2006.09.001openalex-snapshot

Structure- and property-based design of factor Xa inhibitors: Pyrrolidin-2-ones with acyclic alanyl amides as P4 motifs

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Residence Times of Water Molecules in the Hydration Sites of Myoglobin

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Optimization of the β-Aminoester class of factor Xa inhibitors. part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity

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Protein–water interactions in a dynamic world

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Structural Basis for Inhibition Promiscuity of Dual Specific Thrombin and Factor Xa Blood Coagulation Inhibitors

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Preparation, Characterization, and the Crystal Structure of the Inhibitor ZK-807834 (CI-1031) Complexed with Factor Xa,

inferredcites →https://doi.org/10.1021/bi0264061openalex-snapshot

Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa ,

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Crystal Structures of Human Factor Xa Complexed with Potent Inhibitors

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Design and Quantitative Structure−Activity Relationship of 3-Amidinobenzyl-1 H -indole-2-carboxamides as Potent, Nonchiral, and Selective Inhibitors of Blood Coagulation Factor Xa

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Molecular Structures of Human Factor Xa Complexed with Ketopiperazine Inhibitors: Preference for a Neutral Group in the S1 Pocket

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Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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Probing the Subpockets of Factor Xa Reveals Two Binding Modes for Inhibitors Based on a 2-Carboxyindole Scaffold: A Study Combining Structure-Activity Relationship and X-ray Crystallography

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Structural Requirements for Factor Xa Inhibition by 3-Oxybenzamides with Neutral P1 Substituents: Combining X-ray Crystallography, 3D-QSAR, and Tailored Scoring Functions

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Discovery of 1-(3‘-Aminobenzisoxazol-5‘-yl)-3-trifluoromethyl-N-[2-fluoro-4- [(2‘-dimethylaminomethyl)imidazol-1-yl]phenyl]-1H-pyrazole-5-carboxyamide Hydrochloride (Razaxaban), a Highly Potent, Selective, and Orally Bioavailable Factor Xa Inhibitor

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Synthesis and Conformational Analysis of a Non-Amidine Factor Xa Inhibitor That Incorporates 5-Methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine as S4 Binding Element

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Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes

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Inhomogeneous Fluid Approach to Solvation Thermodynamics. 1. Theory

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Generalized Born Model Based on a Surface Integral Formulation

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Molecular mechanics methods for predicting protein–ligand binding

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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models

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Polymorphic transitions in single crystals: A new molecular dynamics method

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Molecular dynamics simulations at constant pressure and/or temperature

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A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters

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Comparison of simple potential functions for simulating liquid water

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Molecular dynamics with coupling to an external bath

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Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems

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A smooth particle mesh Ewald method

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding

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Structural basis for chemical inhibition of human blood coagulation factor Xa

inferredcites →https://doi.org/10.1074/jbc.271.47.29988openalex-snapshot

X-ray Structure of Active Site-inhibited Clotting Factor Xa

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Constant pressure molecular dynamics for molecular systems

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Direct entropy calculation from computer simulation of liquids

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How many water molecules can be detected by protein crystallography?

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The Entropic Cost of Bound Water in Crystals and Biomolecules

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A New Approach to the Theory of Classical Fluids. III

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Oral, Direct Factor Xa Inhibitors in Development for the Prevention and Treatment of Thromboembolic Diseases

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(R)-3-Amidinophenylalanine-Derived Inhibitors of Factor Xa with a Novel Active-Site Binding Mode

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inferred← citeshttps://doi.org/10.1007/s10822-012-9575-9openalex-snapshot

Docking performance of the glide program as evaluated on the Astex and DUD datasets: a complete set of glide SP results and selected results for a new scoring function integrating WaterMap and glide

inferred← citeshttps://doi.org/10.1007/s10822-012-9590-xopenalex-snapshot

Virtual fragment screening: exploration of MM-PBSA re-scoring

inferred← citeshttps://doi.org/10.1007/s10822-012-9620-8openalex-snapshot

Free enthalpies of replacing water molecules in protein binding pockets

inferred← citeshttps://doi.org/10.1007/s10822-013-9644-8openalex-snapshot

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

inferred← citeshttps://doi.org/10.1007/s10822-015-9866-zopenalex-snapshot

WONKA: objective novel complex analysis for ensembles of protein–ligand structures

inferred← citeshttps://doi.org/10.1007/s10822-017-0072-zopenalex-snapshot

Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort

inferred← citeshttps://doi.org/10.1007/s10822-017-0075-9openalex-snapshot

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

inferred← citeshttps://doi.org/10.1007/s10822-019-00187-yopenalex-snapshot

Water molecules in protein–ligand interfaces. Evaluation of software tools and SAR comparison

inferred← citeshttps://doi.org/10.1007/s10822-020-00341-xopenalex-snapshot

An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets

inferred← citeshttps://doi.org/10.1007/s10822-020-00344-8openalex-snapshot

Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo

inferred← citeshttps://doi.org/10.1007/s10822-021-00377-7openalex-snapshot

Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein–ligand interactions and quantitative structure–activity relationship studies

inferred← citeshttps://doi.org/10.1007/s10822-021-00406-5openalex-snapshot

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

inferred← citeshttps://doi.org/10.1007/s10822-021-00416-3openalex-snapshot

Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method

inferred← citeshttps://doi.org/10.1007/s10822-022-00492-zopenalex-snapshot

Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin

inferred← citeshttps://doi.org/10.1007/s10822-026-00846-xopenalex-snapshot

Residue‑resolved dynamically averaged interaction analysis of direct factor Xa inhibitors by MD‑FMO combination calculations

inferred← citeshttps://doi.org/10.1007/s11030-022-10470-0openalex-snapshot

Designing of potent anti-diabetic molecules by targeting SIK2 using computational approaches

inferred← citeshttps://doi.org/10.1007/s11172-026-4954-xopenalex-snapshot

Structure-based pharmacophore modeling approaches using probe-based methods

inferred← citeshttps://doi.org/10.1007/s12272-015-0640-5openalex-snapshot

Role of computer-aided drug design in modern drug discovery

inferred← citeshttps://doi.org/10.1016/b978-0-08-101129-4.00001-1openalex-snapshot

Profiling Drug Binding by Thermodynamics

inferred← citeshttps://doi.org/10.1016/b978-0-12-374920-8.00910-3openalex-snapshot

9.7 Molecular Modeling and Simulations of Transporter Proteins – The Transmembrane Allosteric Machinery

inferred← citeshttps://doi.org/10.1016/b978-0-12-381274-2.00015-7openalex-snapshot

Lead Generation and Examples

inferred← citeshttps://doi.org/10.1016/b978-0-12-396521-9.00004-8openalex-snapshot

Structural Biology and Anticancer Drug Design

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12312-1openalex-snapshot

Drug Discovery Technologies: Current and Future Trends

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12346-7openalex-snapshot

2/3D Pharmacophore Definitions and Their Application

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12353-4openalex-snapshot

Lessons and Successes in the Use of Molecular Fields

inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12358-3openalex-snapshot

Modeling and Design for Membrane Protein Targets

inferred← citeshttps://doi.org/10.1016/b978-0-12-820472-6.00208-5openalex-snapshot

Computational Medicinal Chemistry to Target GPCRs

inferred← citeshttps://doi.org/10.1016/b978-0-12-820546-4.00008-8openalex-snapshot

Water mapping: Analysis of binding site spaces to enhance binding

inferred← citeshttps://doi.org/10.1016/b978-0-12-821748-1.00009-9openalex-snapshot

Advances in structure-based drug design

inferred← citeshttps://doi.org/10.1016/b978-0-323-99507-8.00020-2openalex-snapshot

Modeling solvent effects and molecular electrostatics

inferred← citeshttps://doi.org/10.1016/b978-0-443-21848-4.00011-xopenalex-snapshot

Application of isothermal titration calorimetry in drug discovery and development

inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00005-4openalex-snapshot

2/3D Pharmacophore definitions and their application

inferred← citeshttps://doi.org/10.1016/b978-0-443-44988-8.00017-4openalex-snapshot

Future trends in structural biology

inferred← citeshttps://doi.org/10.1016/b978-0-443-45105-8.00011-1openalex-snapshot

SGR-1505: A MALT1 inhibitor in clinical trials for the treatment of relapsed/refractory B-cell malignancies

inferred← citeshttps://doi.org/10.1016/b978-0-443-49253-2.00010-6openalex-snapshot

Molecular dynamics and its integration with docking studies

inferred← citeshttps://doi.org/10.1016/bs.pmch.2021.01.004openalex-snapshot

Use of molecular docking computational tools in drug discovery

inferred← citeshttps://doi.org/10.1016/j.bbrc.2026.154710openalex-snapshot

In silico discovery and cellular validation of PBM-342: a novel PPAR-β/δ modulator for skeletal muscle differentiation

inferred← citeshttps://doi.org/10.1016/j.bcp.2017.10.014openalex-snapshot

Kinetics of human cannabinoid 1 (CB1) receptor antagonists: Structure-kinetics relationships (SKR) and implications for insurmountable antagonism

inferred← citeshttps://doi.org/10.1016/j.bmc.2015.05.028openalex-snapshot

Discovery of 3,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-2(1H)-one derivatives as novel JAK inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmc.2017.05.004openalex-snapshot

Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator

inferred← citeshttps://doi.org/10.1016/j.bmc.2018.08.005openalex-snapshot

Discovery and structural characterization of peficitinib (ASP015K) as a novel and potent JAK inhibitor

inferred← citeshttps://doi.org/10.1016/j.bmc.2024.117932openalex-snapshot

Design of a potent and selective dual JAK1/TYK2 inhibitor

inferred← citeshttps://doi.org/10.1016/j.bmcl.2010.09.019openalex-snapshot

Identification of optimum computational protocols for modeling the aryl hydrocarbon receptor (AHR) and its interaction with ligands

inferred← citeshttps://doi.org/10.1016/j.bmcl.2011.01.140openalex-snapshot

Structure–activity relationship study of 2,4-diaminothiazoles as Cdk5/p25 kinase inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmcl.2011.08.119openalex-snapshot

The successful quest for oral factor Xa inhibitors; learnings for all of medicinal chemistry?

inferred← citeshttps://doi.org/10.1016/j.bmcl.2014.01.062openalex-snapshot

Synthesis, biological evaluation, hydration site thermodynamics, and chemical reactivity analysis of α-keto substituted peptidomimetics for the inhibition of Plasmodium falciparum

inferred← citeshttps://doi.org/10.1016/j.bmcl.2015.11.093openalex-snapshot

Preparation and optimization of pyrazolo[1,5-a]pyrimidines as new potent PDE4 inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmcl.2016.09.077openalex-snapshot

Synthesis and optimization of furano[3,2-d]pyrimidines as selective spleen tyrosine kinase (Syk) inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmcl.2017.11.031openalex-snapshot

Structure-based design, synthesis, and binding mode analysis of novel and potent chymase inhibitors

inferred← citeshttps://doi.org/10.1016/j.bmcl.2018.05.061openalex-snapshot

Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands

inferred← citeshttps://doi.org/10.1016/j.bmcl.2022.129047openalex-snapshot

Identification of potent and selective inhibitors of PKR via virtual screening and traditional design

inferred← citeshttps://doi.org/10.1016/j.bmcl.2023.129331openalex-snapshot

Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors

inferred← citeshttps://doi.org/10.1016/j.bpj.2011.03.033openalex-snapshot

Role of Hydration in Collagen Recognition by Bacterial Adhesins

inferred← citeshttps://doi.org/10.1016/j.bpj.2012.06.003openalex-snapshot

Drying Transition in the Hydrophobic Gate of the GLIC Channel Blocks Ion Conduction

inferred← citeshttps://doi.org/10.1016/j.bpj.2020.05.020openalex-snapshot

Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations

inferred← citeshttps://doi.org/10.1016/j.bpj.2022.12.019openalex-snapshot

Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction

inferred← citeshttps://doi.org/10.1016/j.bpj.2026.06.036openalex-snapshot

Quantifying the peripheral surface information entropy from conformational ensembles of globular protein-peptide complexes

inferred← citeshttps://doi.org/10.1016/j.carres.2011.02.016openalex-snapshot

Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor

inferred← citeshttps://doi.org/10.1016/j.chemphyslip.2022.105227openalex-snapshot

Experimental and theoretical investigations into the mechanism of interactions between membrane-bound fatty acids and their binding protein: A model system to investigate the behavior of lipid acyl chains in contact with proteins

inferred← citeshttps://doi.org/10.1016/j.chempr.2017.07.009openalex-snapshot

A Water-Bridged Cysteine-Cysteine Redox Regulation Mechanism in Bacterial Protein Tyrosine Phosphatases

inferred← citeshttps://doi.org/10.1016/j.coph.2016.07.001openalex-snapshot

Molecular dynamics techniques for modeling G protein-coupled receptors

inferred← citeshttps://doi.org/10.1016/j.cplett.2017.08.063openalex-snapshot

Assessment of CCSD(T), MP2, and DFT methods for the calculations of structures and interaction energies of the peptide backbone with water molecules

inferred← citeshttps://doi.org/10.1016/j.cplett.2022.139470openalex-snapshot

Molecular dynamics study of quercetin families and its derivative compounds from Carica papaya leaf as breast cancer inhibitors

inferred← citeshttps://doi.org/10.1016/j.ddtec.2021.08.005openalex-snapshot

Fragment-to-lead tailored in silico design

inferred← citeshttps://doi.org/10.1016/j.drudis.2016.05.009openalex-snapshot

Water, water, everywhere… It's time to stop and think

inferred← citeshttps://doi.org/10.1016/j.ejmech.2014.10.043openalex-snapshot

Malonate-based inhibitors of mammalian serine racemase: Kinetic characterization and structure-based computational study

inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.03.059openalex-snapshot

Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors

inferred← citeshttps://doi.org/10.1016/j.ejmech.2016.12.023openalex-snapshot

Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines

inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113777openalex-snapshot

Structure-activity relationships of agonists for the orphan G protein-coupled receptor GPR27

inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.115347openalex-snapshot

Shifting the selectivity of pyrido[2,3-d]pyrimidin-7(8H)-one inhibitors towards the salt-inducible kinase (SIK) subfamily

inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.116671openalex-snapshot

Novel compounds with dual inhibition activity against SARS-CoV-2 critical enzymes RdRp and human TMPRSS2

inferred← citeshttps://doi.org/10.1016/j.ejps.2017.07.002openalex-snapshot

Design, synthesis, and biological evaluation of 2,4-dihydropyrano[2,3-c]pyrazole derivatives as autotaxin inhibitors

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.141703openalex-snapshot

Evaluating the polypharmacological potency of FEDPN from ChEMBL BioAssays against lung cancer EGFR, ALK, TrkA and KRAS proteins

inferred← citeshttps://doi.org/10.1016/j.insi.2026.100299openalex-snapshot

Hydration site analysis and molecular simulations highlight drug repurposing opportunities for TRIM24 bromodomain inhibition

inferred← citeshttps://doi.org/10.1016/j.jbc.2021.101529openalex-snapshot

Efficient incorporation and template-dependent polymerase inhibition are major determinants for the broad-spectrum antiviral activity of remdesivir

inferred← citeshttps://doi.org/10.1016/j.jbc.2023.105456openalex-snapshot

Resolving binding pathways and solvation thermodynamics of plant hormone receptors

inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107514openalex-snapshot

Mechanism and spectrum of inhibition of a 4′-cyano modified nucleotide analog against diverse RNA polymerases of prototypic respiratory RNA viruses

inferred← citeshttps://doi.org/10.1016/j.jmb.2010.05.020openalex-snapshot

Structural and Thermodynamic Characterization of the TYK2 and JAK3 Kinase Domains in Complex with CP-690550 and CMP-6

inferred← citeshttps://doi.org/10.1016/j.jmb.2013.09.039openalex-snapshot

A Simple Atomic-Level Hydrophobicity Scale Reveals Protein Interfacial Structure

inferred← citeshttps://doi.org/10.1016/j.jmgm.2010.05.004openalex-snapshot

Understanding the stereospecific interactions of 3-deoxyphosphatidylinositol derivatives with the PTEN phosphatase domain

inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.04.010openalex-snapshot

Using thermodynamic integration MD simulation to compute relative protein–ligand binding free energy of a GSK3β kinase inhibitor and its analogs

inferred← citeshttps://doi.org/10.1016/j.jmgm.2018.04.011openalex-snapshot

Analysis of the influence of simulation parameters on biomolecule-linked water networks

inferred← citeshttps://doi.org/10.1016/j.jpba.2018.09.002openalex-snapshot

Chemical, biological and molecular modelling analyses to probe into the pharmacological potential of Antidesma madagascariense Lam.: A multifunctional agent for developing novel therapeutic formulations

inferred← citeshttps://doi.org/10.1016/j.molliq.2021.116338openalex-snapshot

Prediction of local thermodynamics of water in and around endo-functionalized molecular tube receptors: An approach using grid inhomogeneous solvation theory

inferred← citeshttps://doi.org/10.1016/j.molliq.2023.122281openalex-snapshot

Molecular insight on hydration of protein tyrosine phosphatase 1B and its complexes with ligands

inferred← citeshttps://doi.org/10.1016/j.molstruc.2010.03.008openalex-snapshot

Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain

inferred← citeshttps://doi.org/10.1016/j.molstruc.2026.146978openalex-snapshot

Design, synthesis, computational study, and biological evaluation of sulphonyl and amide tethered ibuprofen-piperazine derivatives as potential anti-inflammatory agents with possible COX-2 interaction

inferred← citeshttps://doi.org/10.1016/j.pharmthera.2014.02.004openalex-snapshot

Unifying Family A GPCR Theories of Activation

inferred← citeshttps://doi.org/10.1016/j.sbi.2008.11.009openalex-snapshot

Computational evaluation of protein–small molecule binding

inferred← citeshttps://doi.org/10.1016/j.sbi.2011.01.010openalex-snapshot

Advances in all atom sampling methods for modeling protein–ligand binding affinities

inferred← citeshttps://doi.org/10.1016/j.sbi.2016.10.007openalex-snapshot

Accelerating drug discovery through tight integration of expert molecular design and predictive scoring

inferred← citeshttps://doi.org/10.1016/j.sbi.2020.08.002openalex-snapshot

The role of water in ligand binding

inferred← citeshttps://doi.org/10.1016/j.str.2009.02.010openalex-snapshot

Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

inferred← citeshttps://doi.org/10.1016/j.str.2020.04.018openalex-snapshot

GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps

inferred← citeshttps://doi.org/10.1016/j.tips.2012.03.004openalex-snapshot

The role of structural information in the discovery of direct thrombin and factor Xa inhibitors

inferred← citeshttps://doi.org/10.1016/j.xpro.2025.104144openalex-snapshot

Protocol for predicting γ-tocotrienol and δ-tocotrienol binding to colorectal cancer-related proteins using Schrödinger’s Maestro and Glide

inferred← citeshttps://doi.org/10.1016/j.ymeth.2014.10.019openalex-snapshot

Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies

inferred← citeshttps://doi.org/10.1017/s0033583511000096openalex-snapshot

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

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