1
|
Verteramo ML, Ignjatović MM, Kumar R, Wernersson S, Ekberg V, Wallerstein J, Carlström G, Chadimová V, Leffler H, Zetterberg F, Logan DT, Ryde U, Akke M, Nilsson UJ. Interplay of halogen bonding and solvation in protein-ligand binding. iScience 2024; 27:109636. [PMID: 38633000 PMCID: PMC11021960 DOI: 10.1016/j.isci.2024.109636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Halogen bonding is increasingly utilized in efforts to achieve high affinity and selectivity of molecules designed to bind proteins, making it paramount to understand the relationship between structure, dynamics, and thermodynamic driving forces. We present a detailed analysis addressing this problem using a series of protein-ligand complexes involving single halogen substitutions - F, Cl, Br, and I - and nearly identical structures. Isothermal titration calorimetry reveals an increasingly favorable binding enthalpy from F to I that correlates with the halogen size and σ-hole electropositive character, but is partially counteracted by unfavorable entropy, which is constant from F to Cl and Br, but worse for I. Consequently, the binding free energy is roughly equal for Cl, Br, and I. QM and solvation-free-energy calculations reflect an intricate balance between halogen bonding, hydrogen bonds, and solvation. These advances have the potential to aid future drug design initiatives involving halogenated compounds.
Collapse
Affiliation(s)
| | | | - Rohit Kumar
- Department of Chemistry, Lund University, Lund, Sweden
| | | | | | | | | | | | - Hakon Leffler
- Microbiology, Immunology, and Glycobiology, Department of Experimental Medicine, Lund University, Lund, Sweden
| | | | | | - Ulf Ryde
- Department of Chemistry, Lund University, Lund, Sweden
| | - Mikael Akke
- Department of Chemistry, Lund University, Lund, Sweden
| | | |
Collapse
|
2
|
Fortuna A, Costa PJ. Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations. J Chem Inf Model 2023; 63:7464-7475. [PMID: 38010191 DOI: 10.1021/acs.jcim.3c01561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Compounds containing halogens can form halogen bonds (XBs) with biological targets such as proteins and membranes due to their anisotropic electrostatic potential. To accurately describe this anisotropy, off-center point-charge (EP) models are commonly used in force field methods, allowing the description of XBs at the molecular mechanics and molecular dynamics level. Various EP implementations have been documented in the literature, and despite being efficient in reproducing protein-ligand geometries and sampling of XBs, it is unclear how well these EP models predict experimental properties such as hydration free energies (ΔGhyd), which are often used to validate force field performance. In this work, we report the first assessment of three EP models using alchemical free energy calculations to predict ΔGhyd values. We show that describing the halogen anisotropy using some EP models can lead to a slight improvement in the prediction of the ΔGhyd when compared with the models without EP, especially for the chlorinated compounds; however, this improvement is not related to the establishment of XBs but is most likely due to the improvement of the sampling of hydrogen bonds. We also highlight the importance of the choice of the EP model, especially for the iodinated molecules, since a slight tendency to improve the prediction is observed for compounds with a larger σ-hole but significantly worse results were obtained for compounds that are weaker XB donors.
Collapse
Affiliation(s)
- Andreia Fortuna
- BioISI─Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, Lisbon 1649-003, Portugal
| | - Paulo J Costa
- BioISI─Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| |
Collapse
|
3
|
Sun Z, He Q, Gong Z, Kalhor P, Huai Z, Liu Z. A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions. Molecules 2023; 28:molecules28073124. [PMID: 37049887 PMCID: PMC10095826 DOI: 10.3390/molecules28073124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.
Collapse
|
4
|
Sakai T, Torii H. Substituent Effect and Its Halogen-Atom Dependence of Halogen Bonding Viewed through Electron Density Changes. Chem Asian J 2023; 18:e202201196. [PMID: 36545823 DOI: 10.1002/asia.202201196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Elucidating how the halogen-bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely-tuned design of functionally important molecules. Here, this problem is tackled by analyzing the electron density differences/changes for variously substituted halobenzenes. It is shown that the anisotropy of the electron distribution around the halogen atom, which is an important factor for halogen-bonding ability, is not much affected by the substituent effect and rather simply depends on the halogen atom, while the partial charge on the halogen atom, which is related to the bond dipole of the C-X bond, is significantly modulated by the substituent effect and gives rise to enhancement of the electrostatic potential on the line extended from the C-X bond. The properties related to the polarization effect are also discussed.
Collapse
Affiliation(s)
- Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course Department of Engineering Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| | - Hajime Torii
- Applied Chemistry and Biochemical Engineering Course Department of Engineering Graduate School of Integrated Science and Technology and Department of Optoelectronics and Nanostructure Science Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| |
Collapse
|
5
|
Fenanir F, Semmeq A, Benguerba Y, Badawi M, Dziurla MA, Amira S, Laouer H. In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes. J Biomol Struct Dyn 2022; 40:11571-11586. [PMID: 34355673 DOI: 10.1080/07391102.2021.1960197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The present study aimed to experimentally identify the essential oil of Algerian Cyperus rotundus L. and to model the interaction of some known anti-inflammatory molecules with two key enzymes involved in inflammation, 5-Lypoxygenase (5-LO) and leukotriene A4 hydrolase (LTA4H). Gas chromatography/gas chromatography-mass spectrometry (GC/GC-MS) revealed that 92.7% of the essential oil contains 35 compounds, including oxygenated sesquiterpenes (44.2%), oxygenated monoterpenes (30.2%), monoterpene hydrocarbons (11.8%) and sesquiterpene hydrocarbons (6.5%). The major identified oxygenated terpenes are humulene oxide II, caryophyllene oxide, khusinol, agarospirol, spathulinol and trans-pinocarveol Myrtenol and α-terpineol are known to exhibit anti-inflammatory activities. Several complexes obtained after docking the natural terpenes with 5-LO and LTA4H have shown strong hydrogen bonding interactions. The best docking energies were found with α-terpineol, Myrtenol and khusinol. The interaction between the natural products and amino-acid residues HIS367, ILE673 and GLN363 appears to be critical for 5-LO inhibition, while the interaction with residues GLU271, HIS295, TYR383, TYR378, GLU318, GLU296 and ASP375 is critical for LTA4H inhibition. Molecular dynamics (MD) trajectories of the selected docked complexes showed stable backbone root mean square deviation (RMSD), supporting the stability of the natural product-enzyme interaction.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fares Fenanir
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| | - Abderrahmane Semmeq
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France
| | - Yacine Benguerba
- Laboratoire des Matériaux Polymères Multiphasiques, LMPMP, Université Ferhat ABBAS, Sétif, Algeria
| | - Michael Badawi
- Laboratoire de Physique et Chimie Théoriques (UMR 7019), CNRS-Université de Lorraine, Saint-Avold, France.,IUT de Moselle-Est, Université de Lorraine, Saint-Avold, France
| | | | - Smain Amira
- Laboratory of Phytotherapy Applied to Chroniques Diseases, University Ferhat Abbas, Sétif, Algeria
| | - Hocine Laouer
- Laboratory of Valorization of Natural and biological Resources, University Ferhat Abbas, Sétif, Algeria
| |
Collapse
|
6
|
Gorges J, Bädorf B, Hansen A, Grimme S. Efficient Computation of the Interaction Energies of Very Large Non-covalently Bound Complexes. Synlett 2022. [DOI: 10.1055/s-0042-1753141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractWe present a new benchmark set consisting of 16 large non-covalently bound systems (LNCI16) ranging from 380 up to 1988 atoms and featuring diverse interaction motives. Gas-phase interaction energies are calculated with various composite DFT, semi-empirical quantum mechanical (SQM), and force field (FF) methods and are evaluated using accurate DFT reference values. Of the employed QM methods, PBEh-3c proves to be the most robust for large systems with a relative mean absolute deviation (relMAD) of 8.5% with respect to the reference interaction energies. r2SCAN-3c yields an even smaller relMAD, at least for the subset of complexes for which the calculation could be converged, but is less robust for systems with smaller HOMO–LUMO gaps. The inclusion of Fock-exchange is therefore important for the description of very large non-covalent interaction (NCI) complexes in the gas phase. GFN2-xTB was found to be the best performer of the SQM methods with an excellent result of only 11.1% deviation. From the assessed force fields, GFN-FF and GAFF achieve the best accuracy. Considering their low computational costs, both can be recommended for routine calculations of very large NCI complexes, with GFN-FF being clearly superior in terms of general applicability. Hence, GFN-FF may be routinely applied in supramolecular synthesis planning.1 Introduction2 The LNCI16 Benchmark Set3 Computational Details4 Generation of Reference Values5 Results and Discussion6 Conclusions
Collapse
|
7
|
Abstract
Generalized force fields (FFs) act as extensions to biomolecular FFs to provide a wide coverage of organic molecules. However, their precise application to an arbitrary molecule presents a separate challenge. We show that MATCH assigns different atom types and bonded and nonbonded parameters than CGenFF, and the AM1-BCC charge model, commonly used with GAFF/GAFF2, does not exactly reproduce the performance of the RESP charge model. The results indicate the need for caution when employing FFs to ensure their integrity with respect to their implementation and validation.
Collapse
Affiliation(s)
- Asuka A. Orr
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Suliman Sharif
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| |
Collapse
|
8
|
Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
Collapse
Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
| |
Collapse
|
9
|
Torii H, Kimura A, Sakai T. Nature of hydrogen-bond-enhanced halogen bonding viewed through electron density changes. Phys Chem Chem Phys 2022; 24:17951-17955. [PMID: 35861167 DOI: 10.1039/d2cp02845j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elucidating the mechanism of how we can achieve fine tuning of intermolecular interaction strength will be helpful for designing functionally important molecules. In the present study, a theoretical analysis is conducted, by examining the electron density changes, for two halogen-bonding iodinated systems whose halogen-bond strengths have been considered to be enhanced by the presence of a hydrogen-bond donating group (termed hydrogen-bond-enhanced halogen bonding). It is shown that, contrary to the expectation obtained from the enhancement of electrostatic potential along the line extended from the C-I bond, the anisotropy of electron distribution on the iodine atom remains nearly the same. This means that the hydrogen bond and halogen bond contribute almost independently and additively to the enhancement of electrostatic potential, indicating the nature of this enhancement and, in a more general sense, the relationship between the strength and the extent of directionality of halogen bonding.
Collapse
Affiliation(s)
- Hajime Torii
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan. .,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Akari Kimura
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
| | - Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
| |
Collapse
|
10
|
Leskourová A, Kolář MH. The effect of off-center σ -hole on the atom-centered partial charges in halogenated molecules. J Comput Chem 2022; 43:864-869. [PMID: 35298034 DOI: 10.1002/jcc.26841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/07/2022]
Abstract
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ -hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ -hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the restricted electrostatic potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The σ -hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.
Collapse
Affiliation(s)
- Aneta Leskourová
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michal H Kolář
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| |
Collapse
|
11
|
Fellowes T, White JM. Simulating chalcogen bonding using molecular mechanics: a pseudoatom approach to model ebselen. J Mol Model 2022; 28:66. [PMID: 35201444 PMCID: PMC8867462 DOI: 10.1007/s00894-021-05023-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Abstract
The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory–optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen. Ebselen is an organoselenium drug that has shown promise for the treatment of a number of conditions. Computational modelling of drug-target complexes is commonly performed to determine the likely mechanism of action, however this is difficult in the case of ebselen, as an important mode of interaction is not simulated using current techniques. We present here an extension to common methods, which accurately captures this interaction. ![]()
Collapse
Affiliation(s)
- Thomas Fellowes
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia.
| | - Jonathan M White
- Bio21 Institute and School of Chemistry, University of Melbourne, Parkville, Australia
| |
Collapse
|
12
|
Forni A, Russo R, Rapeti G, Pieraccini S, Sironi M. Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene. Molecules 2021; 26:7126. [PMID: 34885707 PMCID: PMC8659280 DOI: 10.3390/molecules26237126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists' community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H2O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group.
Collapse
Affiliation(s)
- Alessandra Forni
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
| | - Rosario Russo
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Giacomo Rapeti
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Stefano Pieraccini
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| | - Maurizio Sironi
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”—CNR, INSTM RU, Via Golgi 19, 20133 Milan, Italy
- Department of Chemistry, Università degli Studi di Milano, INSTM RU, Via Golgi 19, 20133 Milano, Italy; (R.R.); (G.R.)
| |
Collapse
|
13
|
Saito K, Torii H. Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride. J Phys Chem B 2021; 125:11742-11750. [PMID: 34662140 DOI: 10.1021/acs.jpcb.1c07211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.
Collapse
|
14
|
Seo B, Lin ZY, Zhao Q, Webb MA, Savoie BM. Topology Automated Force-Field Interactions (TAFFI): A Framework for Developing Transferable Force Fields. J Chem Inf Model 2021; 61:5013-5027. [PMID: 34533949 DOI: 10.1021/acs.jcim.1c00491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Force-field development has undergone a revolution in the past decade with the proliferation of quantum chemistry based parametrizations and the introduction of machine learning approximations of the atomistic potential energy surface. Nevertheless, transferable force fields with broad coverage of organic chemical space remain necessary for applications in materials and chemical discovery where throughput, consistency, and computational cost are paramount. Here, we introduce a force-field development framework called Topology Automated Force-Field Interactions (TAFFI) for developing transferable force fields of varying complexity against an extensible database of quantum chemistry calculations. TAFFI formalizes the concept of atom typing and makes it the basis for generating systematic training data that maintains a one-to-one correspondence with force-field terms. This feature makes TAFFI arbitrarily extensible to new chemistries while maintaining internal consistency and transferability. As a demonstration of TAFFI, we have developed a fixed-charge force-field, TAFFI-gen, from scratch that includes coverage for common organic functional groups that is comparable to established transferable force fields. The performance of TAFFI-gen was benchmarked against OPLS and GAFF for reproducing several experimental properties of 87 organic liquids. The consistent performance of these force fields, despite their distinct origins, validates the TAFFI framework while also providing evidence of the representability limitations of fixed-charge force fields.
Collapse
Affiliation(s)
- Bumjoon Seo
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Zih-Yu Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Qiyuan Zhao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| | - Michael A Webb
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08540, United States
| | - Brett M Savoie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47906, United States
| |
Collapse
|
15
|
Frontera A, Bauzá A. Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases. Org Biomol Chem 2021; 19:6858-6864. [PMID: 34319314 DOI: 10.1039/d1ob01212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.
Collapse
Affiliation(s)
- Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
| | | |
Collapse
|
16
|
Ford MC, Rappé AK, Ho PS. A Reduced Generalized Force Field for Biological Halogen Bonds. J Chem Theory Comput 2021; 17:5369-5378. [PMID: 34232642 DOI: 10.1021/acs.jctc.1c00362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The halogen bond (or X-bond) is a noncovalent interaction that is increasingly recognized as an important design tool for engineering protein-ligand interactions and controlling the structures of proteins and nucleic acids. In the past decade, there have been significant efforts to characterize the structure-energy relationships of this interaction in macromolecules. Progress in the computational modeling of X-bonds in biological molecules, however, has lagged behind these experimental studies, with most molecular mechanics/dynamics-based simulation methods not properly treating the properties of the X-bond. We had previously derived a force field for biological X-bonds (ffBXB) based on a set of potential energy functions that describe the anisotropic electrostatic and shape properties of halogens participating in X-bonds. Although fairly accurate for reproducing the energies within biomolecular systems, including X-bonds engineered into a DNA junction, the ffBXB with its seven variable parameters was considered to be too unwieldy for general applications. In the current study, we have generalized the ffBXB by reducing the number of variables to just one for each halogen type and show that this remaining electrostatic variable can be estimated for any new halogenated molecule through a standard restricted electrostatic potential calculation of atomic charges. In addition, we have generalized the ffBXB for both nucleic acids and proteins. As a proof of principle, we have parameterized this reduced and more general ffBXB against the AMBER force field. The resulting parameter set was shown to accurately recapitulate the quantum mechanical landscape and experimental interaction energies of X-bonds incorporated into DNA junction and T4 lysozyme model systems. Thus, this reduced and generalized ffBXB is more readily adaptable for incorporation into classical molecular mechanics/dynamics algorithms, including those commonly used to design inhibitors against therapeutic targets in medicinal chemistry and materials in biomolecular engineering.
Collapse
Affiliation(s)
- Melissa Coates Ford
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| | - Anthony K Rappé
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, United States
| |
Collapse
|
17
|
Fortuna A, Costa PJ. Optimized Halogen Atomic Radii for PBSA Calculations Using Off-Center Point Charges. J Chem Inf Model 2021; 61:3361-3375. [PMID: 34185532 DOI: 10.1021/acs.jcim.1c00177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In force-field methods, the usage of off-center point charges, also called extra points (EPs), is a common strategy to tackle the anisotropy of the electrostatic potential of covalently bonded halogens (X), thus allowing the description of halogen bonds (XBs) at the molecular mechanics/molecular dynamics (MM/MD) level. Diverse EP implementations exist in the literature differing on the charge sets and/or the X-EP distances. Poisson-Boltzmann and surface area (PBSA) calculations can be used to obtain solvation free energies (ΔGsolv) of small molecules, often to compute binding free energies (ΔGbind) at the MM-PBSA level. This method depends, among other parameters, on the empirical assignment of atomic radii (PB radii). Given the multiplicity of off-center point-charge models and the lack of specific PB radii for halogens compatible with such implementations, in this work, we assessed the performance of PBSA calculations for the estimation of ΔGsolv values in water (ΔGhyd), also conducting an optimization of the halogen PB radii (Cl, Br, and I) for each EP model. We not only expand the usage of EP models in the scope of the general AMBER force field (GAFF) but also provide the first optimized halogen PB radii in the context of the CHARMM general force field (CGenFF), thus contributing to improving the description of halogenated compounds in PBSA calculations.
Collapse
Affiliation(s)
- Andreia Fortuna
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal.,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Paulo J Costa
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
| |
Collapse
|
18
|
Nunes RS, Vila-Viçosa D, Costa PJ. Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions. J Am Chem Soc 2021; 143:4253-4267. [DOI: 10.1021/jacs.0c12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rafael Santana Nunes
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| | - Paulo J. Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016 Lisboa, Portugal
| |
Collapse
|
19
|
Robidas R, Legault CY, Huber SM. A low cost, high accuracy method for halogen bonding complexes. Phys Chem Chem Phys 2021; 23:3041-3049. [PMID: 33480927 DOI: 10.1039/d0cp05614f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The ONIOM scheme M052X/[Def2TZVP+Def2TZVPD.ECP(I)]:AM1 is shown to represent halogen bond (XB) geometries nearly as well as DFT while being more than two orders of magnitude faster in systems containing >40 atoms. This finding is shown to hold for 40 XB donors, which cover most known backbones, and for a range of neutral and anionic Lewis bases. Complexation free energies can be accurately computed using these geometries and a single-point energy calculation at the DFT level. This approach circumvents the unfavorable scaling of computing time associated with modeling large systems involving halogen bonding.
Collapse
Affiliation(s)
- Raphaël Robidas
- Department of Chemistry, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada.
| | - Claude Y Legault
- Department of Chemistry, Université de Sherbrooke, 2500 boul. de l'Université, Sherbrooke, Québec J1K 2R1, Canada.
| | - Stefan M Huber
- Department of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| |
Collapse
|
20
|
Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| |
Collapse
|
21
|
Saito K, Izumi R, Torii H. Dissecting the electric quadrupolar and polarization effects operating in halogen bonding through electron density analysis with a focus on bromine. J Chem Phys 2020; 153:174302. [PMID: 33167658 DOI: 10.1063/5.0021615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The form of the electron density change (or difference) is usable as a kind of fingerprint of the electronic structural origin or mechanism that gives rise to intermolecular interactions. Here, this method is applied to halogen-bonding brominated systems to dissect the electric quadrupolar effect (arising from the anisotropic distribution of the valence electrons and intrinsic to the s2px 2py 2pz electronic configuration) and the polarization effect (induced by a partial negative charge of the halogen-bond accepting atom). It is shown that a suitable location of the "extra point" for placing a partial positive charge to represent the former is crucial and is clearly found from the electron density difference from the spherically isotropic Br- ion, while the latter consists of the dipolar polarization of the Br atom and the delocalized polarization of the whole molecule. A practical way for application to molecular dynamics simulations, etc., to represent these two factors is discussed.
Collapse
Affiliation(s)
- Kento Saito
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Ryoma Izumi
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Hajime Torii
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| |
Collapse
|
22
|
Nizi MG, Desantis J, Nakatani Y, Massari S, Mazzarella MA, Shetye G, Sabatini S, Barreca ML, Manfroni G, Felicetti T, Rushton-Green R, Hards K, Latacz G, Satała G, Bojarski AJ, Cecchetti V, Kolář MH, Handzlik J, Cook GM, Franzblau SG, Tabarrini O. Antitubercular polyhalogenated phenothiazines and phenoselenazine with reduced binding to CNS receptors. Eur J Med Chem 2020; 201:112420. [DOI: 10.1016/j.ejmech.2020.112420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/21/2020] [Accepted: 05/02/2020] [Indexed: 02/08/2023]
|
23
|
Campetella M, De Mitri N, Prampolini G. Automated parameterization of quantum-mechanically derived force-fields including explicit sigma holes: A pathway to energetic and structural features of halogen bonds in gas and condensed phase. J Chem Phys 2020; 153:044106. [PMID: 32752684 DOI: 10.1063/5.0014280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions of the systems of interest, it would be therefore desirable to increase the FF accuracy maintaining the simplicity of the standard Lennard-Jones (LJ) plus point charge description to avoid an excessive computational cost. A simple yet effective strategy consists in introducing a number of virtual sites able to mimic the so-called "explicit σ-hole." In this work, we present an automated FF parameterization strategy based on a global optimization of both LJ and charge parameters with respect to accurate quantum mechanical data, purposely computed for the system under investigation. As a test case, we report on two homologue series, characterized either by weak or strong XBs, namely, the di-halogenated methanes and the mono-, di-, and tri-substituted acetonitriles, taking into consideration Cl, Br, and I substituents. The resulting quantum mechanically derived FFs are validated for each compound in the gas and in the condensed phase by comparing them to general purpose and specific FFs without virtual sites and to highly accurate reference quantum mechanical data. The results strongly support the adoption of the specific FFs with virtual sites, which overcome the other investigated models in representing both gas phase energetics and the structural patterns of the liquid phase structure related to the presence of XBs.
Collapse
Affiliation(s)
- Marco Campetella
- Institut des Nanosciences de Paris, Sorbonne Université, CNRS, UMR7588, F-75252 Paris, France
| | - Nicola De Mitri
- Enthought Ltd., Broers Building, 21 JJ Thomson Avenue, Cambridge CB3 0FA, United Kingdom
| | - Giacomo Prampolini
- Istituto di Chimica dei Composti Organo Metallici (ICCOM), CNR Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| |
Collapse
|
24
|
Rational Design, Synthesis, Characterization and Evaluation of Iodinated 4,4'-Bipyridines as New Transthyretin Fibrillogenesis Inhibitors. Molecules 2020; 25:molecules25092213. [PMID: 32397334 PMCID: PMC7248964 DOI: 10.3390/molecules25092213] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023] Open
Abstract
The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine structure is proposed as a novel chemical scaffold for the design of new transthyretin (TTR) fibrillogenesis inhibitors. In the frame of a proof-of-principle exploration, four chiral 3,3',5,5'-tetrachloro-2-iodo-2'-substituted-4,4'- bipyridines were rationally designed and prepared from a simple trihalopyridine in three steps, including a Cu-catalysed Finkelstein reaction to introduce iodine atoms on the heteroaromatic scaffold, and a Pd-catalysed coupling reaction to install the 2'-substituent. The corresponding racemates, along with other five chiral 4,4'-bipyridines containing halogens as substituents, were enantioseparated by high-performance liquid chromatography in order to obtain pure enantiomer pairs. All stereoisomers were tested against the amyloid fibril formation (FF) of wild type (WT)-TTR and two mutant variants, V30M and Y78F, in acid mediated aggregation experiments. Among the 4,4'-bipyridine derivatives, interesting inhibition activity was obtained for both enantiomers of the 3,3',5,5'-tetrachloro-2'-(4-hydroxyphenyl)-2-iodo-4,4'-bipyridine. In silico docking studies were carried out in order to explore possible binding modes of the 4,4'-bipyridine derivatives into the TTR. The gained results point out the importance of the right combination of H-bond sites and the presence of iodine as halogen-bond donor. Both experimental and theoretical evidences pave the way for the utilization of the iodinated 4,4'-bipyridine core as template to design new promising inhibitors of TTR amyloidogenesis.
Collapse
|
25
|
El Khoury L, El Hage K, Piquemal JP, Fermandjian S, Maroun RG, Gresh N, Hobaika Z. Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities. PEERJ PHYSICAL CHEMISTRY 2019. [DOI: 10.7717/peerj-pchem.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, which are little, if at all, mutation-prone. We report experimental results of anisotropy fluorescence titrations of viral DNA by these three drugs. These show the DTG > EVG > RAL ranking of their inhibitory activities of the intasome to correspond to that of their free energies of binding, ∆Gs, to retroviral DNA, and that such a ranking is only governed by the binding enthalpies, ∆H, the entropy undergoing marginal variations. We sought whether this ranking might be reproduced through quantum chemistry (QC) Density Functional Theory calculations of intermolecular interaction energies between simplified models consisting of sole halobenzene ring and the highly conserved retroviral nucleobases G4 and C16. These calculations showed that binding of EVG has a small preference over DTG, while RAL ranked third. This indicates that additional interactions of the diketoacid parts of the drugs with DNA could be necessary to further enable preferential binding of DTG. The corresponding ∆Etotvalues computed with a polarizable molecular mechanics/dynamics procedure, Sum of Interactions Between Fragments Ab initio computed (SIBFA), showed good correlations with this ∆E(QC) ranking. These validations are an important step toward the use of polarizable molecular dynamics simulations on DTG or EVG derivatives in their complexes with the complete intasome, an application now motivated and enabled by the advent of currently developed and improved massively parallel software.
Collapse
Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Present address: Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Krystel El Hage
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
- Present address: Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, INSERM U829, Université Evry-Val d’Essonne, Evry, France
| | - Jean-Philip Piquemal
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Institut Universitaire de France, Paris, France
| | - Serge Fermandjian
- Chemistry and Biology Nucleo(s)tides and Immunology for Therapy (CBNIT), UMR 8601 CNRS, UFR Biomedicale, Paris, France
| | - Richard G. Maroun
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR7616 CNRS, Sorbonne Université, Paris, France
| | - Zeina Hobaika
- UR EGP, Centre d’Analyses et de Recherche, Faculté des Sciences, Université Saint-Joseph de Beyrouth, Beirut, Lebanon
| |
Collapse
|
26
|
Puttreddy R, Rautiainen JM, Mäkelä T, Rissanen K. Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine
N
‐Oxide Complexes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Rakesh Puttreddy
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - J. Mikko Rautiainen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Toni Mäkelä
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Kari Rissanen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| |
Collapse
|
27
|
Puttreddy R, Rautiainen JM, Mäkelä T, Rissanen K. Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine
N
‐Oxide Complexes. Angew Chem Int Ed Engl 2019; 58:18610-18618. [DOI: 10.1002/anie.201909759] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/27/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Rakesh Puttreddy
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - J. Mikko Rautiainen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Toni Mäkelä
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| | - Kari Rissanen
- University of JyvaskylaDepartment of Chemistry P.O. BOX 35 40014 Jyväskylä Finland
| |
Collapse
|
28
|
Nunes R, Vila-Viçosa D, Costa PJ. Tackling Halogenated Species with PBSA: Effect of Emulating the σ-Hole. J Chem Theory Comput 2019; 15:4241-4251. [PMID: 31142112 DOI: 10.1021/acs.jctc.9b00106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To model halogen-bond phenomena using classical force fields, an extra point (EP) of charge is frequently introduced at a given distance from the halogen (X) to emulate the σ-hole. The resulting molecular dynamics (MD) trajectories can be used in subsequent molecular mechanics (MM) combined with Poisson-Boltzmann and surface area calculations (PBSA) to estimate protein-ligand binding free energies (Δ Gbind). While EP addition improves the MM/MD description of halogen-containing systems, its effect on the calculation of solvation free energies (Δ Gsolv) using the PBSA approach is yet to be assessed. As the PBSA calculations depend, among other parameters, on the empirical assignment of radii (PB radii), a problematic issue arises, since standard halogen radii are smaller than the typical X···EP distances, thus placing the EP within the solvent dielectric. Herein, we took a common literature EP parametrization scheme, which uses X···EP = Rmin and RESP charges in the context of GAFF, and performed a comprehensive study on the performance of PBSA (using three different setups) in the calculation of Δ Gsolv values for 142 halogenated compounds (bearing Cl, Br, or I) for which the experimental values are known. By conducting an optimization (minimizing the error against experimental values), we provide a new optimized set of halogen PB radii, for each PBSA setup, that should be used in the context of the aforementioned scenario. A simultaneous optimization of PB radii and X···EP distances shows that a wide range of distance/radius pairs can be used without significant loss of accuracy, therefore laying the basis for expanding this halogen radii optimization strategy to other force fields and EP implementations. As ligand Δ Gsolv estimation is an important term in the determination of protein-ligand Δ Gbind, this work is particularly relevant in the framework of structure-based virtual screening and related computer-aided drug design routines.
Collapse
|
29
|
Costa PJ, Nunes R, Vila-Viçosa D. Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design. Expert Opin Drug Discov 2019; 14:805-820. [PMID: 31131651 DOI: 10.1080/17460441.2019.1619692] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction: Halogens have a prominent role in drug design. Often used as a mean to improve ADME properties, they are also becoming a tool in protein-ligand recognition given their ability to form a non-covalent interaction, termed halogen bond, where halogens act as electrophilic species interacting with electron-rich partners. Rational drug design of halogen-bonding lead molecules requires an accurate description of halocarbon-protein complexes by computational tools though not all methods are able to tackle this non-covalent interaction. Areas covered: The authors present a review of computational methodologies that can be used to properly describe halogen bonds in the context of protein-ligand complexes, providing also insights on how these methods can be used in the context of computer-aided drug design. Expert opinion: Although in the last few years many computational tools, ranging from fast screening methods to the more expensive QM calculations, have been developed to tackle the halogen bonding phenomenon, they are not yet standard in the literature. This will eventually change as official software distributions are including support for halogen bonding in their methods. Tackling desolvation of halogenated species seems to be a good strategy to improve the accuracy of computational methods, that will be more commonly used prior to laboratory work in the future.
Collapse
Affiliation(s)
- Paulo J Costa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Rafael Nunes
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| | - Diogo Vila-Viçosa
- a Centro de Quı́mica e Bioquı́mica, Departamento de Quı́mica e Bioquı́mica , Faculdade de Ciências da Universidade de Lisboa, Campo Grande , Lisboa , Portugal.,b University of Lisboa, Faculty of Sciences , BioISI - Biosystems & Integrative Sciences Institute , Lisboa , Portugal
| |
Collapse
|
30
|
Mahmoud AH, Yang Y, Lill MA. Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ-Dynamics. J Chem Theory Comput 2019; 15:3272-3287. [PMID: 30933496 DOI: 10.1021/acs.jctc.8b00940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amr H. Mahmoud
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Ying Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| |
Collapse
|
31
|
Peluso P, Dessì A, Dallocchio R, Mamane V, Cossu S. Recent studies of docking and molecular dynamics simulation for liquid-phase enantioseparations. Electrophoresis 2019; 40:1881-1896. [PMID: 30710444 DOI: 10.1002/elps.201800493] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/16/2022]
Abstract
Liquid-phase enantioseparations have been fruitfully applied in several fields of science. Various applications along with technical and theoretical advancements contributed to increase significantly the knowledge in this area. Nowadays, chromatographic techniques, in particular HPLC on chiral stationary phase, are considered as mature technologies. In the last thirty years, CE has been also recognized as one of the most versatile technique for analytical scale separation of enantiomers. Despite the huge number of papers published in these fields, understanding mechanistic details of the stereoselective interaction between selector and selectand is still an open issue, in particular for high-molecular weight chiral selectors like polysaccharide derivatives. With the ever growing improvement of computer facilities, hardware and software, computational techniques have become a basic tool in enantioseparation science. In this field, molecular docking and dynamics simulations proved to be extremely adaptable to model and visualize at molecular level the spatial proximity of interacting molecules in order to predict retention, selectivity, enantiomer elution order, and profile noncovalent interaction patterns underlying the recognition process. On this basis, topics and trends in using docking and molecular dynamics as theoretical complement of experimental LC and CE chiral separations are described herein. The basic concepts of these computational strategies and seminal studies performed over time are presented, with a specific focus on literature published between 2015 and November 2018. A systematic compilation of all published literature has not been attempted.
Collapse
Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Alessandro Dessì
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Roberto Dallocchio
- Istituto di Chimica Biomolecolare ICB CNR - Sede Secondaria di Sassari, Sassari, Sardegna, Italy
| | - Victor Mamane
- Institut de Chimie de Strasbourg, Strasbourg, Alsace, France
| | - Sergio Cossu
- Dipartimento di Scienze Molecolari e Nanosistemi DSMN, Università Ca' Foscari Venezia, Mestre Venezia, Veneto, Italy
| |
Collapse
|
32
|
Titov OI, Shulga DA, Palyulin VA. Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding. J Chem Theory Comput 2018; 15:1159-1167. [DOI: 10.1021/acs.jctc.8b00739] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Oleg I. Titov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A. Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vladimir A. Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
33
|
Yang Y, Mahmoud AH, Lill MA. Modeling of Halogen–Protein Interactions in Co-Solvent Molecular Dynamics Simulations. J Chem Inf Model 2018; 59:38-42. [PMID: 30525593 DOI: 10.1021/acs.jcim.8b00806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ying Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Amr H. Mahmoud
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47906, United States
| |
Collapse
|
34
|
Hagler AT. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics. J Comput Aided Mol Des 2018; 33:205-264. [DOI: 10.1007/s10822-018-0134-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023]
|
35
|
Franchini D, Dapiaggi F, Pieraccini S, Forni A, Sironi M. Halogen bonding in the framework of classical force fields: The case of chlorine. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
36
|
Nunes R, Vila-Viçosa D, Machuqueiro M, Costa PJ. Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field. J Chem Theory Comput 2018; 14:5383-5392. [PMID: 30215528 DOI: 10.1021/acs.jctc.8b00278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Halogen bonds (XBs) are non-covalent interactions in which halogens (X), acting as electrophiles, interact with Lewis bases. XBs are able to mediate protein-ligand recognition and therefore play an important role in rational drug design. In this context, the development of molecular modeling tools that can tackle XBs is paramount. XBs are predominantly explained by the existence of a positive region on the electrostatic potential of X named the σ-hole. Typically, with molecular mechanics force fields, this region is modeled using a charged extra point (EP) linked to X along the R-X covalent bond axis. In this work, we developed the first EP-based strategy for GROMOS force fields (specifically GROMOS 54A7) using bacteriophage T4 lysozyme in complex with both iodobenzene and iodopentafluorobenzene as a prototype system. Several EP parametrization schemes were tested by adding a virtual interaction site to ligand topologies retrieved from the Automated Topology Builder (ATB) and Repository. Contrary to previous approaches using other force fields, our analysis is based on the capability of each parametrization scheme to sample XBs during MD simulations. Our results indicate that the implementation of an EP at a distance from iodine corresponding to Rmin provides a good qualitative description of XBs in MD simulations, supporting the compatibility of our approach with the GROMOS 54A7 force field.
Collapse
Affiliation(s)
- Rafael Nunes
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal.,Centro de Química Estrutural, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal
| | - Diogo Vila-Viçosa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| | - Paulo J Costa
- Centro de Química e Bioquímica, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, 1749-016 Lisboa , Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências , Universidade de Lisboa , Campo Grande, C8 bdg, 1749-016 Lisboa , Portugal
| |
Collapse
|
37
|
Kurczab R, Canale V, Satała G, Zajdel P, Bojarski AJ. Amino Acid Hot Spots of Halogen Bonding: A Combined Theoretical and Experimental Case Study of the 5-HT 7 Receptor. J Med Chem 2018; 61:8717-8733. [PMID: 30188719 DOI: 10.1021/acs.jmedchem.8b00828] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A computational approach combining a structure-activity relationship library of halogenated and the corresponding unsubstituted ligands (called XSAR) with QM-based molecular docking and binding free energy calculations was used to search for amino acids frequently targeted by halogen bonding (hot spots) in a 5-HT7R as a case study. The procedure identified two sets of hot spots, extracellular (D2.65, T2.64, and E7.35) and transmembrane (C3.36, T5.39, and S5.42), which were further verified by a synthesized library of halogenated arylsulfonamide derivatives of (aryloxy)ethylpiperidines. It was found that a halogen bond formed between T5.39 and a bromine atom at 3-position of the aryloxy fragment caused the most remarkable, 35-fold increase in binding affinity for 5-HT7R when compared to the nonhalogenated analog. The proposed paradigm of halogen bonding hot spots was additionally verified on D4 dopamine receptor showing that it can be used in rational drug design/optimization for any protein target.
Collapse
Affiliation(s)
- Rafał Kurczab
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Vittorio Canale
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Grzegorz Satała
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| | - Paweł Zajdel
- Department of Medicinal Chemistry , Jagiellonian University Medical College , 9 Medyczna Street , 30-688 Krakow , Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry , Institute of Pharmacology, Polish Academy of Sciences , 12 Smętna Street , 31-343 Krakow , Poland
| |
Collapse
|
38
|
Role and nature of halogen bonding in inhibitor⋅⋅⋅receptor complexes for drug discovery: casein kinase-2 (CK2) inhibition as a case study. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2207-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
39
|
Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J Chem Inf Model 2017; 57:2911-2937. [PMID: 29243483 DOI: 10.1021/acs.jcim.7b00564] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives, using a combination of retrospective literature examples and prospective studies from drug discovery projects. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative binding free energy simulations, with a focus on real-world drug discovery applications. We offer guidelines for improving the accuracy of RBFE simulations, especially for challenging cases, and emphasize unresolved issues that could be improved by further research in the field.
Collapse
Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens , 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Bryce Allen
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| |
Collapse
|
40
|
Antipov SV, Bhattacharyya S, El Hage K, Xu ZH, Meuwly M, Rothlisberger U, Vaníček J. Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061509. [PMID: 29376107 PMCID: PMC5758379 DOI: 10.1063/1.4996559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.
Collapse
Affiliation(s)
- Sergey V Antipov
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Swarnendu Bhattacharyya
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Zhen-Hao Xu
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Jiří Vaníček
- Laboratory of Theoretical Physical Chemistry, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| |
Collapse
|
41
|
Batista-Romero FA, Pajón-Suárez P, Roncero O, Hernández-Lamoneda R. Nature of the guest-host interactions for dibromine in the T, P, and H clathrate cages. J Chem Phys 2017; 147:154301. [DOI: 10.1063/1.4993465] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
42
|
Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges. J Comput Aided Mol Des 2017; 32:287-297. [PMID: 28918599 DOI: 10.1007/s10822-017-0065-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/08/2017] [Indexed: 10/18/2022]
Abstract
The goal of virtual screening is to generate a substantially reduced and enriched subset of compounds from a large virtual chemistry space. Critical in these efforts are methods to properly rank the binding affinity of compounds. Prospective evaluations of ranking strategies in the D3R grand challenges show that for targets with deep pockets the best correlations (Spearman ρ ~ 0.5) were obtained by our submissions that docked compounds to the holo-receptors with the most chemically similar ligand. On the other hand, for targets with open pockets using multiple receptor structures is not a good strategy. Instead, docking to a single optimal receptor led to the best correlations (Spearman ρ ~ 0.5), and overall performs better than any other method. Yet, choosing a suboptimal receptor for crossdocking can significantly undermine the affinity rankings. Our submissions that evaluated the free energy of congeneric compounds were also among the best in the community experiment. Error bars of around 1 kcal/mol are still too large to significantly improve the overall rankings. Collectively, our top of the line predictions show that automated virtual screening with rigid receptors perform better than flexible docking and other more complex methods.
Collapse
|
43
|
Looking Back, Looking Forward at Halogen Bonding in Drug Discovery. Molecules 2017; 22:molecules22091397. [PMID: 28837116 PMCID: PMC6151711 DOI: 10.3390/molecules22091397] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/18/2017] [Indexed: 11/25/2022] Open
Abstract
Halogen bonding has emerged at the forefront of advances in improving ligand: receptor interactions. In particular the newfound ability of this extant non-covalent-bonding phenomena has revolutionized computational approaches to drug discovery while simultaneously reenergizing synthetic approaches to the field. Here we survey, via examples of classical applications involving halogen atoms in pharmaceutical compounds and their biological hosts, the unique advantages that halogen atoms offer as both Lewis acids and Lewis bases.
Collapse
|
44
|
Yan XC, Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization. J Phys Chem B 2017. [PMID: 28627890 DOI: 10.1021/acs.jpcb.7b04233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional noncovalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops a new model, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and noncovalent energetics from reliable quantum mechanical calculations, and electrostatic potentials. Significant improvements are obtained for computed free energies of hydration, reducing the mean unsigned errors from ca. 1.4 to 0.4-0.7 kcal/mol. Enhanced accuracy in directionality and energetics is also obtained for molecular complexes with sulfur-containing hydrogen and halogen bonds. Moreover, the new model reproduces the unusual conformational preferences of sulfur-containing compounds with 1,4-intramolecular chalcogen bonds. Transferability of the new force field parameters to cysteine and methionine is verified via molecular dynamic simulations of blocked dipeptides. The study demonstrates the effectiveness of using off-atom charge sites to address electronic anisotropy, and provides a parametrization methodology that can be applied to other systems.
Collapse
Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Michael J Robertson
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
45
|
Halogen bonding in medicinal chemistry: from observation to prediction. Future Med Chem 2017; 9:637-640. [DOI: 10.4155/fmc-2017-0052] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|
46
|
Rowe RK, Ho PS. Relationships between hydrogen bonds and halogen bonds in biological systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:255-264. [PMID: 28362290 DOI: 10.1107/s2052520617003109] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.
Collapse
Affiliation(s)
- Rhianon K Rowe
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
| |
Collapse
|
47
|
Santos LA, da Cunha EFF, Ramalho TC. Toward the Classical Description of Halogen Bonds: A Quantum Based Generalized Empirical Potential for Fluorine, Chlorine, and Bromine. J Phys Chem A 2017; 121:2442-2451. [DOI: 10.1021/acs.jpca.6b13112] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Lucas A. Santos
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Elaine F. F. da Cunha
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, CEP 37200-000 Lavras, Minas Gerais, Brazil
- Center for Basic
and Applied Research, University Hradec Kralove, Hradec Kralove, Czech Republic
| |
Collapse
|
48
|
Kurczab R. The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:188-194. [DOI: 10.1107/s205252061700138x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/27/2017] [Indexed: 11/10/2022]
Abstract
The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular docking with binding free-energy calculations was successfully used to reproduce the X-ray geometries of protein–ligand complexes with halogen bonding. The procedure involves quantum-polarized ligand docking (QPLD) to obtain the QM-derived ligand atomic charges in the protein environment at the B3PW91/cc-pVTZ level and the MM/GBSA (generalized-Born/surface area) algorithm to calculate the binding free energies of resultant complexes. The performance was validated using a set of 106 X-ray complexes and compared with the Glide and AutoDock VinaXB scoring functions in terms of RMSD and the reconstruction of halogen-bond geometry (distance and σ-hole angle). The results revealed that docking and scoring using the QPLD–GBSA procedure outperformed the remaining scoring functions in the majority of instances. Additionally, a comparison of the orientation of the top ranked binding poses calculated using the fixed atomic charges of ligands obtained from force-field parameterization and by QM calculations in the protein environment provides strong evidence that the use of QM-derived charges is significant.
Collapse
|
49
|
Alcaraz-Torres A, Gamboa-Suárez A, Bernal-Uruchurtu MI. Is Br2 hydration hydrophobic? J Chem Phys 2017; 146:084501. [DOI: 10.1063/1.4975688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Alcaraz-Torres
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
| | - A. Gamboa-Suárez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
| | - M. I. Bernal-Uruchurtu
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad 1001, Cuernavaca, Morelos 62209,
México
| |
Collapse
|
50
|
Tiwari MK, Vanka K. Exploiting directional long range secondary forces for regulating electrostatics-dominated noncovalent interactions. Chem Sci 2017; 8:1378-1390. [PMID: 28451279 PMCID: PMC5361874 DOI: 10.1039/c6sc03642b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022] Open
Abstract
It has been well established that long range secondary electrostatic interactions (SEIs) have a significant effect on the stability of supramolecular complexes. However, general rules for exploiting SEIs in the rational design of diverse supramolecular complexes have been difficult to obtain. In this work, we outline a quantum chemical approach for understanding the strength of electrostatic interactions. This approach is seen to provide excellent correlation between the electrostatic force and the binding energy between two partners in hydrogen-bonded complexes, as well as that between two ions in ion-pair complexes. Furthermore, we illustrate how the understanding of the binding allows for the rational design of new complexes where the association constant between the two partners can be increased or decreased, as desired, by several orders of magnitude. Hence, the current work showcases a general, simple and powerful method of understanding and exploiting long range secondary electrostatic interactions.
Collapse
Affiliation(s)
- Mrityunjay K Tiwari
- Physical and Material Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune-411008 , Maharashtra , India .
| | - Kumar Vanka
- Physical and Material Chemistry Division , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pashan , Pune-411008 , Maharashtra , India .
| |
Collapse
|