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Orgován Z, Ferenczy GG, Steinbrecher T, Szilágyi B, Bajusz D, Keserű GM. Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors. J Comput Aided Mol Des 2018; 32:331-345. [PMID: 29335871 DOI: 10.1007/s10822-018-0097-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/06/2018] [Indexed: 01/16/2023]
Abstract
Optimization of fragment size D-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.
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Mártonfalvi Z, Bianco P, Naftz K, Ferenczy GG, Kellermayer M. Force generation by titin folding. Protein Sci 2017; 26:1380-1390. [PMID: 28097712 DOI: 10.1002/pro.3117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/08/2017] [Accepted: 01/09/2017] [Indexed: 12/19/2022]
Abstract
Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (<10 pN), extension fluctuated without resolvable discrete events. In position-clamp experiments, the time-dependent force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles.
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Williams G, Ferenczy GG, Ulander J, Keserű GM. Binding thermodynamics discriminates fragments from druglike compounds: a thermodynamic description of fragment-based drug discovery. Drug Discov Today 2016; 22:681-689. [PMID: 27916639 DOI: 10.1016/j.drudis.2016.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/12/2016] [Accepted: 11/24/2016] [Indexed: 01/18/2023]
Abstract
Small is beautiful - reducing the size and complexity of chemical starting points for drug design allows better sampling of chemical space, reveals the most energetically important interactions within protein-binding sites and can lead to improvements in the physicochemical properties of the final drug. The impact of fragment-based drug discovery (FBDD) on recent drug discovery projects and our improved knowledge of the structural and thermodynamic details of ligand binding has prompted us to explore the relationships between ligand-binding thermodynamics and FBDD. Information on binding thermodynamics can give insights into the contributions to protein-ligand interactions and could therefore be used to prioritise compounds with a high degree of specificity in forming key interactions.
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Bata I, Tömösközi Z, Buzder-Lantos P, Vasas A, Szeleczky G, Balázs L, Barta-Bodor V, Ferenczy GG. II. Discovery of a novel series of CXCR3 antagonists with a beta amino acid core. Bioorg Med Chem Lett 2016; 26:5429-5437. [DOI: 10.1016/j.bmcl.2016.10.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 01/22/2023]
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Bata I, Tömösközi Z, Buzder-Lantos P, Vasas A, Szeleczky G, Bátori S, Barta-Bodor V, Balázs L, Ferenczy GG. I. Discovery of a novel series of CXCR3 antagonists. Multiparametric optimization of N , N -disubstituted benzylamines. Bioorg Med Chem Lett 2016; 26:5418-5428. [DOI: 10.1016/j.bmcl.2016.10.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 12/15/2022]
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Bajusz D, Ferenczy GG, Keserű GM. Ensemble docking-based virtual screening yields novel spirocyclic JAK1 inhibitors. J Mol Graph Model 2016; 70:275-283. [PMID: 27771575 DOI: 10.1016/j.jmgm.2016.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/12/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Small molecule inhibition of Janus kinases (JAKs) has been demonstrated as a viable strategy for the treatment of various inflammatory conditions and continues to emerge in cancer-related indications. In this study, a large supplier database was screened to identify novel chemistry starting points for JAK1. The docking-based screening was followed up by testing ten hit compounds experimentally, out of which five have displayed single-digit micromolar and submicromolar IC50 values on JAK1. Thus, the study was concluded with the discovery of five novel JAK inhibitors from a tiny screening deck with a remarkable hitrate of 50%. The results have highlighted spirocyclic pyrrolopyrimidines with submicromolar JAK1 IC50 values and a preference for JAK1 over JAK2 as potential starting points in developing a novel class of JAK1 inhibitors.
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Hégely B, Nagy PR, Ferenczy GG, Kállay M. Exact density functional and wave function embedding schemes based on orbital localization. J Chem Phys 2016. [DOI: 10.1063/1.4960177] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Martin YC, Abagyan R, Ferenczy GG, Gillet VJ, Oprea TI, Ulander J, Winkler D, Zefirov NS. Glossary of terms used in computational drug design, part II (IUPAC Recommendations 2015). PURE APPL CHEM 2016. [DOI: 10.1515/pac-2012-1204] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractComputational drug design is a rapidly changing field that plays an increasingly important role in medicinal chemistry. Since the publication of the first glossary in 1997, substantial changes have occurred in both medicinal chemistry and computational drug design. This has resulted in the use of many new terms and the consequent necessity to update the previous glossary. For this purpose a Working Party of eight experts was assembled. They produced explanatory definitions of more than 150 new and revised terms.
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Kelemen ÁA, Kiss R, Ferenczy GG, Kovács L, Flachner B, Lőrincz Z, Keserű GM. Structure-Based Consensus Scoring Scheme for Selecting Class A Aminergic GPCR Fragments. J Chem Inf Model 2016; 56:412-22. [PMID: 26760056 DOI: 10.1021/acs.jcim.5b00598] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aminergic G-protein coupled receptors (GPRCs) represent well-known targets of central nervous-system related diseases. In this study a structure-based consensus virtual screening scheme was developed for designing targeted fragment libraries against class A aminergic GPCRs. Nine representative aminergic GPCR structures were selected by first clustering available X-ray structures and then choosing the one in each cluster that performs best in self-docking calculations. A consensus scoring protocol was developed using known promiscuous aminergic ligands and decoys as a training set. The consensus score (FrACS-fragment aminergic consensus score) calculated for the optimized protein ensemble showed improved enrichments in most cases as compared to stand-alone structures. Retrospective validation was carried out on public screening data for aminergic targets (5-HT1 serotonin receptor, TA1 trace-amine receptor) showing 8-17-fold enrichments using an ensemble of aminergic receptor structures. The performance of the structure based FrACS in combination with our ligand-based prefilter (FrAGS) was investigated both in a retrospective validation on the ChEMBL database and in a prospective validation on an in-house fragment library. In prospective validation virtual fragment hits were tested on 5-HT6 serotonin receptors not involved in the development of FrACS. Six out of the 36 experimentally tested fragments exhibited remarkable antagonist efficacies, and 4 showed IC50 values in the low micromolar or submicromolar range in a cell-based assay. Both retrospective and prospective validations revealed that the methodology is suitable for designing focused class A GPCR fragment libraries from large screening decks, commercial compound collections, or virtual databases.
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Abstract
Detailed thermodynamic analysis of fragment binding revealed that unlike drug-like compounds, fragments bind with significant enthalpic preference.
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Bajusz D, Ferenczy GG, Keserű GM. Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening. J Chem Inf Model 2015; 56:234-47. [DOI: 10.1021/acs.jcim.5b00634] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Ferenczy GG. Computation of Drug-Binding Thermodynamics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bajusz D, Ferenczy GG, Keserű GM. Property-based characterization of kinase-like ligand space for library design and virtual screening. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00253b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A property-based desirability scoring scheme has been developed for kinase-focused library design and ligand-based pre-screening of large compound sets.
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Kelemen ÁA, Ferenczy GG, Keserű GM. Erratum to: A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. J Comput Aided Mol Des 2014; 29:67. [PMID: 25395250 DOI: 10.1007/s10822-014-9812-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kelemen ÁA, Ferenczy GG, Keserű GM. A desirability function-based scoring scheme for selecting fragment-like class A aminergic GPCR ligands. J Comput Aided Mol Des 2014; 29:59-66. [DOI: 10.1007/s10822-014-9804-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/10/2014] [Indexed: 01/10/2023]
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Ferenczy GG. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation. J Comput Chem 2013; 34:854-61. [PMID: 23281055 DOI: 10.1002/jcc.23210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 11/08/2012] [Accepted: 11/23/2012] [Indexed: 12/13/2022]
Abstract
Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods.
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Ferenczy GG, Keserű GM. How Are Fragments Optimized? A Retrospective Analysis of 145 Fragment Optimizations. J Med Chem 2013; 56:2478-86. [DOI: 10.1021/jm301851v] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Ferenczy GG. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation. J Comput Chem 2013; 34:862-9. [PMID: 23288700 DOI: 10.1002/jcc.23209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 11/08/2012] [Accepted: 11/23/2012] [Indexed: 01/03/2023]
Abstract
The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.
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Abstract
The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.
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Ferenczy GG, Keserű GM. Thermodynamics guided lead discovery and optimization. Drug Discov Today 2010; 15:919-32. [DOI: 10.1016/j.drudis.2010.08.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/13/2010] [Accepted: 08/20/2010] [Indexed: 11/28/2022]
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Ferenczy GG, Adams WH. Optimization of selected molecular orbitals in group basis sets. J Chem Phys 2009; 130:134108. [DOI: 10.1063/1.3096690] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Illingworth CJR, Parkes KEB, Snell CR, Ferenczy GG, Reynolds CA. Toward a Consistent Treatment of Polarization in Model QM/MM Calculations. J Phys Chem A 2008; 112:12151-6. [DOI: 10.1021/jp710168q] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Illingworth CJR, Gooding SR, Winn PJ, Jones GA, Ferenczy GG, Reynolds CA. Classical Polarization in Hybrid QM/MM Methods. J Phys Chem A 2006; 110:6487-97. [PMID: 16706406 DOI: 10.1021/jp046944i] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have presented a method for modeling polarization in hybrid QM/MM calculations. The method, which expresses the induced dipoles as a set of "induced" charges, is based on the induced dipole approach and methodology for calculating potential-derived point charges from distributed multipole series. The method has the advantage that the same methodology can be used to determine the induced charges and the potential derived charges and so both sets of charges are rigorously defined within the same framework. This underlying link with the wave function makes the method particularly suitable for use in hybrid QM/MM calculations. Here we assess the importance of explicit polarization in the classical part of a QM/MM system with regard to improving the classical description and the consequent effects on the quantum description. The main advantages of the induced charge approach are that the method is readily interfaced with quantum mechanical methods and that induced charges are more readily interpreted than induced dipoles. The ease of interpretation is illustrated by analysis of the charges involved in dimeric and trimeric hydrogen bonded systems. The method for treating the MM polarization has been validated by a regression analysis of the charges induced in both the QM and MM systems against those derived from full quantum mechanical calculations. The method has also been validated using two energy decomposition approaches, which show that MM polarization makes a significant and reliable contribution to the QM - MM interaction energy in a hybrid system. The distance dependency of the induced charges is investigated in calculations on methylsuccinyl-Ala-Ala-Pro-Ala chlormethyl ketone interacting with human neutrophil elastase and propranolol interacting with asparagine residues in a model of the beta(2)-adrenergic receptor.
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