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DOE OSTI2024

Fingerprinting Interactions between Proteins and Ligands for Facilitating Machine Learning in Drug Discovery

Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein–ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the vast chemical space. Computational approaches, notably quantitative structure–activity/property relationship analysis, have gained prominence. Molecular fingerprints encode molecular structures and serve as property profiles, which are essential in drug discovery. While two-dimensional (2D) fingerprints are commonly used, three-dimensional (3D) structural interaction fingerprints offer enhanced structural features specific to target proteins. Machine learning models trained on interaction fingerprints enable precise binding prediction. Recent focus has shifted to structure-based predictive modeling, with machine-learning scoring functions excelling due to feature engineering guided by key interactions. Notably, 3D interaction fingerprints are gaining ground due to their robustness. Various structural interaction fingerprints have been developed and used in drug discovery, each with unique capabilities. This review recapitulates the developed structural interaction fingerprints and provides two case studies to illustrate the power of interaction fingerprint-driven machine learning. The first elucidates structure–activity relationships in β2 adrenoceptor ligands, demonstrating the ability to differentiate agonists and antagonists. The second employs a retrosynthesis-based pre-trained molecular representation to predict protein–ligand dissociation rates, offering insights into binding kinetics. Despite remarkable progress, challenges persist in interpreting complex machine learning models built on 3D fingerprints, emphasizing the need for strategies to make predictions interpretable. Binding site plasticity and induced fit effects pose additional complexities. Interaction fingerprints are promising but require continued research to harness their full potential.

3D structural interaction fingerprints↗

DOE OSTI2022

Lattice dynamics of high-pressure hydrides studied by inelastic neutron scattering

Due to the small mass and anomalously large neutron scattering cross-section of proton (about 80 barns compared to a few barns for other nuclei), inelastic neutron scattering is considered as one of the most effective tools in studying optical vibrations of hydrogen atoms in metal hydrides. The current review is focused on the binary hydrides of 3d- and 4d-metals of groups VI–VIII, which were produced at high hydrogen pressures of several gigapascals in relatively large quantities of hundreds of mg, quenched to low temperature and studied by INS ex situ at ambient pressure with high statistical accuracy. One of the unusual effects revealed by INS is a strong increase in the strength of the metal-hydrogen interactions with decreasing atomic number of the d-metal accompanied by an increase in the Me-H distance. Based on the available experimental results, the spectra g(E) of the phonon density of states and temperature dependencies CV(T) of the heat capacity at constant volume at T up to 1000 K have been derived in this paper and presented both in the figures and in digital form. This provides the reference data for the theoretical investigations of the crystal structures and compositions of new practically important hydrides giving the opportunity to validate calculation methods by comparing the calculated g(E) and CV(T) with the accurate experimental dependencies for the binary hydrides. Recent INS studies showed [R.A. Klein et al., J. Alloy. Compd. 894 (2022) 162381] that the fingerprints of anomalously short H-H separations of 1.6 Å violating the “2 Å rule” can be easily and unambiguously identified in the complex INS spectra of quaternary hydrides (La,Ce)NiInH 1+x . This makes neutron spectroscopy an attractive means for obtaining valuable data in the search for novel hydrides with a record high hydrogen capacity.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2019

Probing ultrafast C–Br bond fission in the UV photochemistry of bromoform with core-to-valence transient absorption spectroscopy

UV pump–extreme UV (XUV) probe femtosecond transient absorption spectroscopy is used to study the 268 nm induced photodissociation dynamics of bromoform (CHBr3). Core-to-valence transitions at the Br(3d) absorption edge (∼70 eV) provide an atomic scale perspective of the reaction, sensitive to changes in the local valence electronic structure, with ultrafast time resolution. The XUV spectra track how the singly occupied molecular orbitals of transient electronic states develop throughout the C–Br bond fission, eventually forming radical Br and CHBr2 products. Complementary ab initio calculations of XUV spectral fingerprints are performed for transient atomic arrangements obtained from sampling excited-state molecular dynamics simulations. C–Br fission along an approximately CS symmetrical reaction pathway leads to a continuous change of electronic orbital characters and atomic arrangements. Two timescales dominate changes in the transient absorption spectra, reflecting the different characteristic motions of the light C and H atoms and the heavy Br atoms. Within the first 40 fs, distortion from C3v symmetry to form a quasiplanar CHBr2 by the displacement of the (light) CH moiety causes significant changes to the valence electronic structure. Displacement of the (heavy) Br atoms is delayed and requires up to ∼300 fs to form separate Br + CHBr2 products. We demonstrate that transitions between the valence-excited (initial) and valence + core-excited (final) state electronic configurations produced by XUV absorption are sensitive to the localization of valence orbitals during bond fission. The change in valence electron-core hole interaction provides a physical explanation for spectral shifts during the process of bond cleavage.

74 ATOMIC AND MOLECULAR PHYSICS↗