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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 2201

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Prof. Dr. Leonid B. Krivdin

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A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, 664033 Irkutsk, Russia
Interests: computational NMR; natural compounds; stereochemical studies
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Dear Colleagues,

Computational studies in chemistry are rapidly developing in parallel with experimental structural scrutiny of natural products and organic molecules of biological origin. Using modern computational methods, it has now become possible to perform spectral assignments and to identify structural misassignments of complex organic compounds. Computational methods thus provide a high level of correlation between calculated and experimental physicochemical and spectral properties, revealing their power to perform structural identification and stereochemical analysis of demanding natural products.

Currently, a number of computational methods are widely used for the elucidation of natural products. Among these methods, besides those based on the Density Functional Theory employing a wide range of functionals combined with various specialized basis sets, there are also pure non-empirical methods such as MP2, SOPPA, SOPPA(CCSD), CCSD, CCSD(T), CCSDT, and more advanced approaches including those at the relativistic level. All computations are carried out while taking into account the requirement of the lowest possible computational demands, which drastically increase with the number of atomic orbitals in the molecule under study. For natural compounds, this is a crucial limitation, which generally precludes the use of the most advanced computational methods for their identification and stereochemical analysis.

This Special Issue aims to showcase cutting-edge developments computational or NMR studies of natural products, whether extracted from natural sources or synthesized in the laboratories. We look forward to receiving your submissions.

Prof. Dr. Leonid B. Krivdin
Guest Editor

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Keywords

computational chemistry
natural products
structural elucidation
Nuclear Magnetic Resonance (NMR)
Density Functional Theory (DFT)

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Research

30 pages, 32997 KB

Open AccessArticle

Molecular Identification and Characterisation of a Spiro-Indoline-Benzoxadiazine Derivative for Photochromic Textile Sensors

by Elżbieta Sąsiadek-Andrzejczak, Malwina Jaszczak-Kuligowska, Marta Safandowska, Marek Kozicki, Bożena Rokita, Laura Florentino-Madiedo, Marcin Barburski, David Ranz and Reyes Mallada

Int. J. Mol. Sci. 2026, 27(11), 4704; https://doi.org/10.3390/ijms27114704 - 23 May 2026

Viewed by 171

Abstract

This paper describes the comprehensive molecular characterisation and application of a commercially available, but structurally undefined, photochromic pigment for the development of textile sensors. The commercial pigment was successfully identified using a multianalytical approach, including analysis using nuclear magnetic resonance (NMR), Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC). The identified pigment, ethyl-3′-methyl-3′-phenyl-1′-(propan-2-yl)-1′,3′-dihydrospiro[[4,1,2]benzoxadiazine-3,2′-indole], was used to develop a textile sensor by screen printing on a natural fibre fabric surface. The developed sensor exhibited a reversible colour change from white to pink upon exposure to UVA radiation (369 nm). The sensor is characterised by high sensitivity with a linear dose–response of 0–0.005 J/cm² and a dynamic range of up to 0.05 J/cm². Furthermore, the sensor’s molecular safety profile was assessed, including elemental composition and cytotoxicity tests on human dermal fibroblasts, which confirmed the sensor’s biocompatibility with occasional skin contact. In addition to its use in decorative and security elements for product authentication, this study demonstrates the sensor’s ability to map the 2D UVA radiation dose distribution. This research highlights the importance of precise molecular identification in the design of functional, safe, and intelligent textile systems. Full article

(This article belongs to the Special Issue Computational Studies of Natural Products)

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22 pages, 2428 KB

Open AccessArticle

Computational Analysis of SPI1 Missense Mutations and ADMET-Guided Molecular Docking of Cinnamic Acid Targeting the PU.1 ETS Domain: Implications for Hematopoietic Dysregulation and Leukemogenesis

by Mariam M. Jaddah, Samer N. Khalaf, Mohammed Mukhles Ahmed and Aisha Abdullah Alshanqiti

Int. J. Mol. Sci. 2026, 27(10), 4278; https://doi.org/10.3390/ijms27104278 - 11 May 2026

Viewed by 315

Abstract

Spi-1 Proto-Oncogene (SPI1) encodes Purine-rich box 1 Transcription Factor (PU.1), a transcription factor of the ETS family that regulates hematopoietic lineage commitment and immune cell differentiation. Alteration of PU.1 dose or ETS domain integrity may interfere with transcriptional programs, which adds to hematopoietic dysregulation and leukemogenesis. Even though changes in SPI1 expression have been associated with acute myeloid leukemia (AML), the structural and regulatory effects of missense mutations at the PU.1 ETS domain have not been entirely studied, and targeting the PU.1 ETS domain by ligands is an area of computational analysis that should be further pursued. To computationally describe deleterious missense variants of SPI1 in terms of structural stability, evolutionary conservation, post-translational modification (PTM) context and interaction networks, and to measure ADMET-mediated molecular docking of cinnamic acid with the PU.1 ETS domain (8EQG) as a potential modulator. Missense nsSNPs were obtained through Ensembl and narrowed down by consensus prediction of pathogenicity (PredictSNP, combining SIFT, PolyPhen, SNAP and PhD-SNP and other tools). InterPro/UniProt was used for domain mapping. SWISS-MODEL was used to produce wild-type and mutant PU.1 versions, which were analyzed on the structural alignment and Cα–Cα displacement parameters in UCSF Chimera (v1.19). The estimation of stability change was carried out with I-Mutant and MUpro. Prediction of PTM sites was done using MusiteDeep and exploration of functional partners was done using STRING. Human, mouse and zebrafish orthologue conservation was measured by means of MAFFT alignment. GEPIA2 was used to compare the expression of SPI1 in AML (TCGA-LAML) and normal tissues (GTEx). AutoDock Vina (grid center 6, −2, −9 A; 20 × 20 × 20 A; 16 exhaustiveness) was used to prepare cinnamic acid and dock it into the PU.1 ETS domain (8EQG), with SwissDock being used for consistency checks. SwissADME and ADMETlab 2.0 were used to predict drug-likeness, pharmacokinetics, and toxicity. Nine missense mutations were routinely considered as deleterious with the majority of them being located in or near the ETS DNA-binding domain. Structural comparisons showed local perturbations of the structure and I189F and H211P yielded the greatest conformational changes between prioritized variants whereas other forms had minimal movements. A predominantly destabilizing trend was supported by stability prediction whereby V241G had the strongest destabilization signal with further destabilizations being predicted in I189F and R259C. PTM mapping revealed several potential regulatory residues (phosphorylation, acetylation, ubiquitination, and methylation), which indicated that there could be crosstalk between the sequence variation and the transcriptional regulation. The SPI1 was placed in a central hematopoietic transcriptional module (containing RUNX1, CEBP members, GATA1 and IRF factors) by the STRING network. The cross-species alignment showed that there was high conservation of a number of the mutation sites, which would support functional constraint at the ETS region. The expression analysis revealed that the level of SPI1 mRNA in AML was significantly elevated compared to normal tissues. Docking also indicated a slight and reproducible interaction of cinnamic acid with the ETS domain (top affinity −4.27 kcal/mol), with a solitary leading polar anchor and supportive hydrophobic interactions, which is akin to interaction between fragments. The ADMET profiling revealed the likelihood of success in the oral drug-likeness and low CYP inhibition liability, as well as signifying the presence of a possible hepatotoxicity signal that needs further confirmation through experiments. Comprehensive computational studies suggest that certain pathogenic variants of SPI1 missense defects, especially in the ETS domain, can result in loss of PU.1 structural stability and regulatory environment, which are in line with the disturbed hematopoietic regulation and AML-related dysregulation. Cinnamic acid demonstrates moderate yet reproducible binding to the PU.1 ETS domain and has an overall favorable developability profile, which indicates that it is better considered as a starting scaffold, as opposed to an active inhibitor. The results give a logical basis of focused biochemical validation and structure-directed optimization of ETS domain modulators in hematologic disease settings. Full article

(This article belongs to the Special Issue Computational Studies of Natural Products)

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24 pages, 3541 KB

Open AccessArticle

Stereochemical Analysis of Natural Products: Bisindole Alkaloids of the Strychnos-Strychnos Type

by Dmitry A. Grigoriev, Valentin A. Semenov, Luc Angenot and Leonid B. Krivdin

Int. J. Mol. Sci. 2026, 27(1), 337; https://doi.org/10.3390/ijms27010337 - 28 Dec 2025

Cited by 1 | Viewed by 728

Abstract

Results of the high-level computational study of 12 bisindole alkaloids of the Strychnos-Strychnos type are reported in addition of that of five retuline-like monomers frequently encountered in moieties constituting dimeric alkaloids. Based on the comparison of theoretical and experimental NMR chemical shifts, a detailed conformational survey of these stereochemically rich natural products containing multiple asymmetric centers was performed. Our original methodology is based on searching multiple conformational states, geometry optimization, and high-level NMR calculations at the DFT level. Taking into account all known experimental chemical shifts together with their calculated values in the natural products under study, a correlation estimate of NMR chemical shifts was performed by using statistical descriptors. In general, a good agreement of the performed calculations with experiment was achieved, which is manifested by the Corrected Mean Absolute Error of about 0.2 ppm for ¹H and 1.9 ppm for ¹³C NMR chemical shifts in this series. Full article

(This article belongs to the Special Issue Computational Studies of Natural Products)

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