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Hydrogen bonding in the crystal structure of molnupiravir Form I, C13H19N3O7

Published online by Cambridge University Press:  16 January 2025

Tawnee M. Ens ,
James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Megan M. Rost ,
Anja Dosen Open the ORCID record for Anja Dosen [Opens in a new window]  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
Tawnee M. Ens
Affiliation:
North Central College, 131 S. Loomis St., Naperville, IL 60540, USA
James A. Kaduk
Affiliation:
North Central College, 131 S. Loomis St., Naperville, IL 60540, USA Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616, USA
Megan M. Rost
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
Anja Dosen*
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: dosen@icdd.com

Abstract

Molnupiravir Form I crystallizes in space group C2 (#5) with a = 6.48110(17), b = 8.71848(19), c = 27.0607(19) Å, β = 91.920(4)°, V = 1528.22(12) Å3, and Z = 4 at 295 K. The crystal structure consists of supramolecular double layers of molecules parallel to the ab-plane. The layer centers consist of hydrogen-bonded rings forming a 2D network and the outer surfaces of isopropyl groups, with van der Waals interactions between the layers. Each O atom acts as an acceptor in at least one hydrogen bond. A strong O–H⋯O hydrogen bond forms between the hydroxyl group of the oxolane ring and the carbonyl group of the oxopyrimidine ring. The other oxolane hydroxyl group forms bifurcated intra- and intermolecular hydrogen bonds. The hydroxylamino group forms an intramolecular O–H⋯N hydrogen bond with an N atom of the oxopyrimidine ring. The amino group forms an intermolecular N–H⋯N hydrogen bond to the same N atom of the ring. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Keywords

molnupiravirLagevrio™crystal structureRietveld refinementdensity functional theory

Information

Type
New Diffraction Data
Information
Powder Diffraction , Volume 40 , Issue 1 , March 2025 , pp. 72 - 75
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This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
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© The Author(s), 2025. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

I. INTRODUCTION

Molnupiravir (Lagevrio) is an FDA-approved antiviral for the treatment of mild to moderate COVID-19, targeting high-risk individuals (Cavazzoni, Reference Cavazzoni2023). It disrupts the RNA-dependent RNA Polymerase (RdRp) enzyme, hindering the coronavirus and RNA replication (Painter et al., Reference Painter, Natchus, Cohen, Holman and Painter2021; Singh et al., Reference Singh, Singh, Singh and Misra2021). This drug inactivates viral replication by accruing deleterious mutations in the RdRp enzyme, rendering the virus ineffective via mutagenesis (Caraco et al., Reference Caraco, Crofoot, Moncada, Galustyan, Musungaie, Payne, Kovalchuk, Gonzalez, Brown, Williams-Diaz, Gao, Strizki, Grobler, Du, Assaid, Paschke, Butterton, Johnson and De Anda2022). The systematic name (CAS Registry Number 2349386-89-4) is [(2R,3S,4R,5R)-3,4-dihydroxy-5-[4-(hydroxyamino)-2-oxopyrimidin-1-yl]oxolan-2-yl]methyl 2-methylpropanoate.

The patent history of molnupiravir has been reviewed by Imran et al. (Reference Imran, Arora, Asdaq, Khan, Alaqel, Alshammari, Alshehri, Alshrari, Ali, Al-shammeri, Alhazmi, Harshan, Alam and Abida2021). A powder pattern for molnupiravir crystal Form A has been reported in Chinese Patent CN112778387 (Xuchun et al., Reference Xuchun, Yiping and Chenchen2021). Powder patterns of Forms I and II are reported in International Patent Application WO 2022/047229 A1 (Bothe et al., Reference Bothe, Brunskill, Lockwood, Newman and Saindane2022). A picture of the molecule in the crystal structure is provided, but atom coordinates are not reported. During the course of this work, the crystal structure was reported by Bade et al. (Reference Bade, Bothe, Sirota, Brunskill, Newman, Zhang, Tan, Zheng, Brito, Poirer, Fier, Xu, Ward, Stone, Lee, Gitter, Bernardoni, Zompa, Luo, Patel, Masiuk, Mora, Ni, Koh, Tarabakija, Liu, Lowinger and Mahmood2023) and Han et al. (Reference Han, Wang, Song, Yao, Tao, Xie, Li, Qu, Wang, Gao, Sun, Wu and Song2024).

This work is part of a project (Kaduk et al., Reference Kaduk, Crowder, Zhong, Fawcett and Suchomel2014) to determine commercial pharmaceutical crystal structures and add high-quality powder diffraction data to the Powder Diffraction File (Kabekkodu et al., Reference Kabekkodu, Dosen and Blanton2024).

II. EXPERIMENTAL AND ANALYSIS

Molnupiravir was a white powder purchased from TargetMol (Batch #226219) and analyzed at 295 K at 11-BM (Antao et al., Reference Antao, Hassan, Wang, Lee and Toby2008; Lee et al., Reference Lee, Shu, Ramanathan, Preissner, Wang, Beno, Von Dreele, Ribaud, Kurtz, Antao, Jiao and Toby2008; Wang et al., Reference Wang, Toby, Lee, Ribaud, Antao, Kurtz, Ramanathan, Von Dreele and Beno2008) at APS using a wavelength of 0.459744(2) Å. The pattern was indexed and the crystal structure was solved independently using Monte Carlo simulated annealing techniques as implemented in FOX (Favre-Nicolin and Černý, Reference Favre-Nicolin and Černý2002), using (sinθ/λ)max = 0.28 Å−1. Rietveld refinement (Figure 1) was carried out using GSAS-II (Toby and Von Dreele, Reference Toby and Von Dreele2013). The y-coordinate of O1 was fixed to define the origin. All non-H bond distances and angles were restrained according to a Mercury/Mogul Geometry Check (Bruno et al., Reference Bruno, Cole, Kessler, Luo, Motherwell, Purkis, Smith, Taylor, Cooper, Harris and Orpen2004; Sykes et al., Reference Sykes, McCabe, Allen, Battle, Bruno and Wood2011). The oxopyrimidine ring was restrained to be planar. Hydrogen atoms were included in calculated positions and recalculated during the refinement using Materials Studio (Dassault Systèmes, 2023). U iso of the carbon, nitrogen, and oxygen atoms were grouped by chemical similarity, while the U iso for H atoms were fixed at 1.3× the U iso of the carbon, nitrogen, and oxygen atoms they are attached to. The final refinement yielded R wp = 0.1231 and GOF = 1.76. The largest features in the normalized error plot are in the shapes of the 001 peaks; the data did not support refining a more complex profile function, hence the relatively high residuals. The largest peak (0.31 Å from O7) and hole (1.91 Å from N10) in the difference Fourier map were 0.23(6) and −0.21(6) eÅ−3, respectively. The crystal structure of molnupiravir was optimized (fixed unit cell) with density functional theory techniques using VASP 6.0 (Kresse and Furthmüller, Reference Kresse and Furthmüller1996) through the MedeA graphical interface (Materials Design, 2023). Single-point density functional theory calculations (fixed experimental cell) and population analysis were carried out using CRYSTAL23 (Erba et al., Reference Erba, Desmaris, Casassa, Civalleri, Donà, Bush, Searle, Maschio, Daga, Cossard, Ribaldone, Ascrizzi, Marana, Flament and Kirtman2023) using base H, C, N, and O sets defined by Gatti et al. (Reference Gatti, Saunders and Roetti1994).

Figure 1.

The Rietveld plot for molnupiravir Form I shows observed data (blue crosses) and the calculated pattern (green line). The cyan curve represents the normalized error, and the red line indicates the background. The vertical scale is multiplied by 20× for 2θ > 1.5°.

III. RESULTS AND DISCUSSION

The root-mean-square Cartesian displacement of the non-H atoms in the Rietveld-refined and VASP-optimized molecules is 0.126 Å, within the normal range for correct structures (van de Streek and Neumann, Reference van de Streek and Neumann2014). The asymmetric unit with the atom numbering is presented in Figure 2. The side chain's displacement parameters are larger than the ring systems, suggesting possible disorder, but no disorder was modeled as an ordered structure is needed for DFT calculations.

Figure 2.

The asymmetric unit of molnupiravir Form I is shown with atom numbering. Atoms are depicted as 50% probability spheroids. Image generated with Mercury (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020).

Most bond distances, bond angles, and torsion angles fall within the normal range indicated by a Mercury/Mogul Geometry check (Macrae et al., Reference Macrae, Sovago, Cottrell, Galek, McCabe, Pidcock, Platings, Shields, Stevens, Towler and Wood2020). Only the N10–C21–N9 114.2° angle (average = 119.7(18), Z-score = 3.3) and torsion angles involving the C14–N8 bond rotation are flagged as unusual. The N10–C21–N9 angle reflects the orientation of the hydroxylamino group and the pyrimidine ring. The torsion angles lie on the tails of broad bimodal distributions of similar torsion angles and reflect the orientation of the oxolane ring and the side chain. The ring and side chain participate in numerous hydrogen bonds, indicating that solid-state interactions are important in determining the observed conformation.

Quantum chemical geometry optimization of the isolated molecule (DFT/B3LYP/6-31G*/water) using Spartan ‘24 (Wavefunction, 2023) indicated that the solid-state conformation is 7.4 kcal mol−1 higher in energy than a local minimum, which has a different orientation of the oxopyrimidine ring. The global minimum-energy conformation (4.1 kcal mol−1 lower in energy) is much more compact, with the isopropyl group close to the oxopyrazine ring.

The crystal structure consists of supramolecular double layers of molnupiravir molecules parallel to the ab-plane. The layers consist of hydrogen-bonded rings, which form a two-dimensional network, while the outer surfaces consist of isopropyl groups, with van der Waals interactions between the layers. The oxopyrimidine ring planes stack parallel along the a-axis. The shortest distance between the ring centroids is 5.44 Å. Analysis of the contributions to the total crystal energy of the structure using the Forcite module of Materials Studio (Dassault Systèmes, 2023) suggests that angle and torsion distortion terms contribute significantly to the intramolecular deformation energy while electrostatic repulsions dominate the intermolecular energy.

Hydrogen bonds are prominent in the crystal structure (Table I). Each O atom acts as an acceptor in at least one hydrogen bond. There is a strong O–H⋯O hydrogen bond between the hydroxyl group O3 and the carbonyl group O5 of the oxopyrimidine ring. Hydroxyl group O2 forms bifurcated hydrogen bonds, one intra- and the other intermolecular. The energies of the O–H⋯O hydrogen bonds were calculated using the correlation of Rammohan and Kaduk (Reference Rammohan and Kaduk2018). The hydroxyl group O7 forms an intramolecular O–H⋯N hydrogen bond to N9. The amino group N10 forms an intermolecular N–H⋯N hydrogen bond to N9. These classical hydrogen bonds result in a two-dimensional network parallel to the ab-plane. Additionally, there are C–H⋯O hydrogen bonds from ring and methyl carbon atoms. The methyl group C23 forms hydrogen bonds to the carboxyl group of side chains in adjacent molecules, so the sidechain–sidechain interactions are more complex than van der Waals.

TABLE I.

Hydrogen bonds (CRYSTAL23) in molnupiravir Form A.

a Intramolecular.

The volume enclosed by the Hirshfeld surface of molnupiravir (Figure 3; Hirshfeld, Reference Hirshfeld1977; Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021) is 376.99 Å3, 98.67% of the unit cell volume suggesting fairly typical packing density. The only significant close contacts (red in Figure 3) involve the hydrogen bonds. The volume/non-hydrogen atom is smaller than normal (17.8 Å3 in the pharmaceuticals we have studied), at 16.6 Å3.

Figure 3.

The Hirshfeld surface of molnupiravir Form I shows intermolecular contacts: blue for longer than van der Waals radii, red for shorter, and white for equal. Image generated with CrystalExplorer (Spackman et al., Reference Spackman, Turner, McKinnon, Wolff, Grimwood, Jayatilaka and Spackman2021).

The Bravais–Friedel–Donnay–Harker (Bravais, Reference Bravais1866; Friedel, Reference Friedel1907; Donnay and Harker, Reference Donnay and Harker1937) morphology suggests that we might expect platy morphology for molnupiravir, with {001} as the major faces. A second-order spherical harmonic model was included in the refinement. The texture index was 1.001, indicating an insignificant preferred orientation in this rotated capillary specimen.

IV. DEPOSITED DATA

The powder pattern of molnupiravir Form I from this synchrotron data set has been submitted to ICDD for the Powder Diffraction File. CIF files from the Rietveld refinement and DFT geometry optimization were also deposited and can be requested at .

ACKNOWLEDGMENTS

Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. This work was partially supported by the International Centre for Diffraction Data. We thank Saul Lapidus for his assistance in the data collection.

CONFLICTS OF INTEREST

The authors have no conflicts of interest to declare.

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Figure 0

Figure 1. The Rietveld plot for molnupiravir Form I shows observed data (blue crosses) and the calculated pattern (green line). The cyan curve represents the normalized error, and the red line indicates the background. The vertical scale is multiplied by 20× for 2θ > 1.5°.

Figure 1

Figure 2. The asymmetric unit of molnupiravir Form I is shown with atom numbering. Atoms are depicted as 50% probability spheroids. Image generated with Mercury (Macrae et al., 2020).

Figure 2

TABLE I. Hydrogen bonds (CRYSTAL23) in molnupiravir Form A.

Figure 3

Figure 3. The Hirshfeld surface of molnupiravir Form I shows intermolecular contacts: blue for longer than van der Waals radii, red for shorter, and white for equal. Image generated with CrystalExplorer (Spackman et al., 2021).