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Parkes A, Ziaee A, O'Reilly E. Evaluating experimental, knowledge-based and computational cocrystal screening methods to advance drug-drug cocrystal fixed-dose combination development. Eur J Pharm Sci 2024; 203:106931. [PMID: 39389169 DOI: 10.1016/j.ejps.2024.106931] [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: 07/15/2024] [Revised: 09/18/2024] [Accepted: 10/07/2024] [Indexed: 10/12/2024]
Abstract
Fixed-dose combinations (FDCs) offer significant advantages to patients and the pharmaceutical industry alike through improved dissolution profiles, synergistic effects and extended patent lifetimes. Identifying whether two active pharmaceutical ingredients have the potential to form a drug-drug cocrystal (DDC) or interact is an essential step in determining the most suitable type of FDC to formulate. The lack of coherent strategies to determine if two active pharmaceutical ingredients that can be co-administered can form a cocrystal, has significantly impacted DDC commercialisation. This review aims to accelerate the development of FDCs and DDCs by evaluating existing experimental, knowledge-based and computational cocrystal screening methods; the background of their development, their application in screening for cocrystals and DDCs, and their limitations are discussed. The evaluation provided in this review will act as a guide for selecting suitable screening methods to accelerate FDC development.
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Affiliation(s)
- Alice Parkes
- Department of Chemical Sciences, SSPC the SFI Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Limerick, Ireland
| | | | - Emmet O'Reilly
- Department of Chemical Sciences, SSPC the SFI Research Centre for Pharmaceuticals, Bernal Institute, University of Limerick, Limerick, Ireland.
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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.
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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
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Jena R, Laha S, Dwarkanath N, Hazra A, Haldar R, Balasubramanian S, Maji TK. Noncovalent interaction guided selectivity of haloaromatic isomers in a flexible porous coordination polymer. Chem Sci 2023; 14:12321-12330. [PMID: 37969590 PMCID: PMC10631220 DOI: 10.1039/d3sc03079b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023] Open
Abstract
Porous, supramolecular structures exhibit preferential encapsulation of guest molecules, primarily by means of differences in the order of (noncovalent) interactions. The encapsulation preferences can be for geometry (dimension and shape) and the chemical nature of the guest. While geometry-based sorting is relatively straightforward using advanced porous materials, designing a "chemical nature" specific host is not. To introduce "chemical specificity", the host must retain an accessible and complementary recognition site. In the case of a supramolecular, porous coordination polymer (PCP) [Zn(o-phen)(ndc)] (o-phen: 1,10-phenanthroline, ndc: 2,6-naphthalenedicarboxylate) host, equipped with an adaptable recognition pocket, we have discovered that the preferential encapsulation of a haloaromatic isomer is not only for dimension and shape, but also for the "chemical nature" of the guest. This selectivity, i.e., preference for the dimension, shape and chemical nature, is not guided by any complementary recognition site, which is commonly required for "chemical specificity". Insights from crystal structures and computational studies unveil that the differences in the different types of noncovalent host-guest interaction strengths, acting in a concerted fashion, yield the unique selectivity.
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Affiliation(s)
- Rohan Jena
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
| | - Subhajit Laha
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
| | - Nimish Dwarkanath
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
| | - Arpan Hazra
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
| | - Ritesh Haldar
- Tata Institute of Fundamental Research Hyderabad Gopanpally Hyderabad 500046 Telangana India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
| | - Tapas Kumar Maji
- Chemistry and Physics of Materials Unit (CPMU), School of Advanced Materials (SAMat) Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur Bangalore-560064 India
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Dwarkanath N, Balasubramanian S. Gate Opening without Volume Change Triggers Cooperative Gas Interactions, Underpins an Isotherm Step in Metal-Organic Frameworks. Inorg Chem 2022; 61:10810-10821. [PMID: 35771063 DOI: 10.1021/acs.inorgchem.2c01053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three halogenated metal-organic frameworks (MOFs) reported recently exhibited a second step in their CO2 gas adsorption isotherms. The emergence of halogen-bonding interactions beyond a threshold gas pressure between the framework halogen and the CO2 guest was conjectured to be the underlying reason for the additional step in the isotherm. Our investigation employing periodic density functional theory calculations did not show significant interactions between the halogen and CO2 molecules. Further, using a combination of DFT-based ab initio molecular dynamics and grand canonical Monte Carlo simulations, we find that the increased separation of framework nitrate pairs facing each other across the pore channel enables the accommodation of an additional CO2 molecule which is further stabilized by cooperative interactions─an observation that facilely explains the second isotherm step. The increased separation between the nitrate groups can occur without any lattice expansion, consistent with experiments. The results point to a structural feature to achieve this isotherm step in MOFs that neither possess large pores nor exhibit large-scale structural changes such as breathing.
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Affiliation(s)
- Nimish Dwarkanath
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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Ochoa-Resendiz D, Gamboa-Suárez A, Hernández-Lamoneda R. Halogen bonding and rotational disorder in chlorine clathrate hydrate cages. J Chem Phys 2022; 156:124302. [DOI: 10.1063/5.0082604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a detailed theoretical characterization of the structure and interactions in dichlorine clathrate hydrate cages. In the case of the dodecahedral cage there is clear evidence of the presence of halogen bonding whereas in the tetrakaidecahedral the expected signatures are there but in a weaker form. Comparison is made with the available structural data from X-ray experiments, where the rotational motion of the dichlorine has been taken into account through Monte Carlo simulations illustrating delocalization effects associated with sampling multiple minima, specifically for the larger cage. Finally, the intermolecular potentials have been calculated with local correlation methods and energy decomposition analysis has been applied to shed light on the nature of the interactions.
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Remsing RC, Klein ML. Molecular Simulation of Covalent Bond Dynamics in Liquid Silicon. J Phys Chem B 2020; 124:3180-3185. [PMID: 32216375 DOI: 10.1021/acs.jpcb.0c01798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent nontrivial effects on liquid-state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio-simulation-based approach for quantifying the structure and dynamics of covalent bonds in condensed phases. Through the examination of structural correlations among silicon nuclei and maximally localized Wannier function centers, we develop a geometric criterion for covalent bonds in liquid Si. We use this to monitor the dynamics of transient covalent bonding in the liquid state and estimate a covalent bond lifetime. We compare covalent bond dynamics to other processes in liquid Si and similar liquids and suggest experiments to measure the covalent bond lifetime.
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Affiliation(s)
- Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Michael L Klein
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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Remsing RC, Klein ML. Lone Pair Rotational Dynamics in Solids. PHYSICAL REVIEW LETTERS 2020; 124:066001. [PMID: 32109086 DOI: 10.1103/physrevlett.124.066001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/20/2020] [Accepted: 01/23/2020] [Indexed: 06/10/2023]
Abstract
Traditional classifications of crystalline phases focus on nuclear degrees of freedom. Through the examination of both electronic and nuclear structure, we introduce the concept of an electronic plastic crystal. Such a material is classified by crystalline nuclear structure, while localized electronic degrees of freedom-here lone pairs-exhibit orientational motion at finite temperatures. This orientational motion is an emergent phenomenon arising from the coupling between electronic structure and polarization fluctuations generated by collective motions, such as phonons. Using ab initio molecular dynamics simulations, we predict the existence of electronic plastic crystal motion in halogen crystals and halide perovskites, and suggest that such motion may be found in a broad range of solids with lone pair electrons. Such fluctuations in the charge density should be observable, in principle, via synchrotron scattering.
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Affiliation(s)
- Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Michael L Klein
- Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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