The biological target of the study is the central event in sickle cell pathology: the polymerization of hemoglobin S. The disease stems from a single point mutation in the beta-globin gene, in which glutamic acid at the sixth position is replaced by valine. When oxygen levels fall, this seemingly small change causes hemoglobin molecules to clump into rigid fibers, deforming red blood cells into their characteristic sickle shape. These rigid cells clog capillaries, a process known as vaso-occlusion, triggering painful crises, hemolysis and progressive organ damage. Repeated cycles of polymerization and depolymerization also generate oxidative stress, depleting nitric oxide in the vasculature and fueling inflammation that involves platelets, neutrophils and the endothelium.

Current therapies reflect the limits of treating a downstream process. Hydroxyurea raises fetal hemoglobin levels and reduces sickling, voxelotor binds hemoglobin reversibly to keep it in its oxygenated state, and crizanlizumab blocks platelet-mediated adhesion. L-glutamine offers antioxidant support, while regular transfusions manage severe cases. The only curative option, hematopoietic stem cell transplantation from a matched sibling donor, is limited by donor scarcity, cost and serious risks including graft-versus-host disease. Gene editing therapies are emerging but remain inaccessible to most patients globally. This therapeutic gap motivated the Indian team to search for small molecules that could directly inhibit hemoglobin S polymerization while simultaneously counteracting oxidative stress.

The researchers chose two pharmacophores with complementary biological credentials. The first is caffeic acid, a phenolic compound found in coffee, wine, tea and propolis, which has documented antioxidant, anti-inflammatory and anti-carcinogenic properties. Previous experimental work showed that caffeic acid increases the delay time for hemoglobin polymerization, a direct anti-sickling effect, and significantly lowers the concentration of ferryl hemoglobin formed during peroxide reactions. The second is phthalimide, whose derivatives, including the thalidomide family, have been shown to increase gamma-globin expression and fetal hemoglobin production while lowering tumor necrosis factor alpha, giving them both anti-sickling and anti-inflammatory potential.

Using an AI-assisted online tool called Mol-Opt, the team generated bioisosteric analogues of both scaffolds, systematically swapping functional groups to improve potency, pharmacokinetics and safety while preserving the molecular features responsible for activity. This yielded 373 candidate analogues across the two series. Each was then screened through a battery of computational filters. The ADMET Lab 3.0 platform predicted absorption, distribution, metabolism, excretion and toxicity parameters, while the Osiris Property Explorer provided drug-likeness and drug-score assessments. Encouragingly, every analogue satisfied Lipinski’s rule of five, the Pfizer rules and, with few exceptions, the Golden Triangle criteria, suggesting the designed molecules occupy drug-like chemical space with reasonable prospects for oral absorption.

The pharmacokinetic and toxicity screens narrowed the field considerably. Among the caffeic acid derivatives, compounds such as C-168, C-2, C-29, C-195 and C-27 stood out for combining high drug scores with low predicted toxicity. Analogue C-2 proved especially notable, showing the lowest hemotoxicity and genotoxicity values in its series. In the phthalimide series, P-60 and P-41 displayed excellent ADME balance with minimal tissue accumulation and very low skin sensitization, although several otherwise promising analogues, including P-155, P-171, P-202 and P-248, were rejected because of alarmingly high predicted genotoxicity, illustrating how computational toxicity screening can eliminate liabilities before any laboratory synthesis takes place.

The decisive test came from molecular docking against the crystal structure of deoxyhemoglobin S, available in the Protein Data Bank under the identifier 2HBS at 2.05 angstrom resolution. Using the Pyrex implementation of AutoDock Vina, the team docked the analogues into the hemoglobin active site and visualized the interactions with ICM Browser Pro. The phthalimide analogue P-2 achieved the study’s best binding affinity at minus 10.4 kilocalories per mole, followed by P-56 at minus 10.3. Among the caffeic acid derivatives, C-2 led with minus 9.0 kilocalories per mole, ahead of C-72 and C-68. For comparison, the approved drugs hydroxyurea, L-glutamine and voxelotor were docked under the same conditions, and the top analogues outperformed them, forming networks of hydrogen bonds and hydrophobic contacts with residues including LYS-66, ASN-102, ASP-99, VAL-98, LEU-28 and PHE-41.

Because a good docking score does not guarantee that a ligand remains bound in the dynamic environment of a real protein, the two lead compounds were subjected to 100-nanosecond molecular dynamics simulations using the Desmond package in the Schrödinger suite. The P-2 hemoglobin complex proved remarkably stable: after an initial equilibration period, the ligand’s root mean square deviation, fitted to the protein, settled within 1.2 to 2.2 angstroms and remained steady for the rest of the simulation. The C-2 complex showed somewhat greater fluctuation, with average protein RMSD values between 0.8 and 3.2 angstroms, but still maintained its binding pose within the active pocket. Contact analysis revealed that the ligands were held in place by a combination of hydrogen bonds, hydrophobic interactions and water bridges involving residues such as PHE-41, LYS-95, VAL-98, ASP-99 and GLU-43, providing a plausible structural basis for sustained anti-sickling activity.

To probe the electronic foundations of the two leads, the researchers performed density functional theory calculations using the ORCA 5.0.4 program at the B3LYP level with the def2-TZVP basis set. Compound C-2 displayed a HOMO energy of minus 8.63 electron volts localized over its catechol pi-system, identifying it as the principal electron-donating region, while its LUMO at minus 5.23 electron volts spread across the nicotinate ring and ester carbonyl groups. The resulting HOMO-LUMO gap of 3.40 electron volts indicates moderate electronic delocalization and efficient charge-transfer pathways, properties associated with reversible electron transfer and enhanced biological activity. Compound P-2 showed a smaller gap of 2.62 electron volts, with the HOMO distributed over its aromatic indole and benzoyl amide regions and the LUMO concentrated at the carbonyl nicotinate position, suggesting good conjugation and moderate chemical reactivity across the amide framework.

The authors conclude that the combined computational workflow, spanning bioisosteric design, ADMET prediction, docking, dynamics and quantum chemistry, has delivered two credible lead candidates, P-2 and C-2, that merit progression toward laboratory validation. Experimental studies to confirm their anti-sickling activity are reportedly underway. As with any purely computational study, the predictions remain hypotheses until synthesis, binding assays and animal or clinical testing are completed, and the high genotoxicity flags on several analogues underline the need for careful optimization. Nevertheless, the work demonstrates how a rational, multi-method in silico pipeline can compress the early stages of drug discovery, potentially cutting costs and timelines for a disease that has waited decades for a truly transformative small-molecule therapy.

Subject of Research: Computational screening of phthalimide and caffeic acid analogues as potential anti-sickling agents for sickle cell disease

Article Title: Computational screening of some newer potential anti-sickling compounds using docking, ADMET, DFT, and molecular dynamics approaches

Article References: Verma, D., Ahirwar, B., Vaishnav, Y., & Gahrewal, M. (2026). Computational screening of some newer potential anti-sickling compounds using docking, ADMET, DFT, and molecular dynamics approaches. Discover Chemistry, 3(1), Article 495. https://doi.org/10.1007/s44371-026-00942-9

Image Credits: AI Generated

DOI: 10.1007/s44371-026-00942-9

Keywords: sickle cell disease, hemoglobin S polymerization, molecular docking, ADMET, molecular dynamics simulation, DFT, bioisosteres, phthalimide, caffeic acid, drug discovery, computer-aided drug design, vaso-occlusion

The research team, led by Charlène Sirvins, Pascale Goupy and Claire Dufour of INRAE in France, focused on four abundant plant phenolic compounds: chlorogenic acid, caffeic acid, ferulic acid and hydroxytyrosol, the principal phenolic aglycone of olives. These molecules are ubiquitous in the human diet, found in coffee, fruits, cereals, olive oil and red wine, and previous work had shown that plant extracts rich in such compounds can reduce volatile N-nitrosamines in dry-cured bacon and sausages. What remained unclear was precisely how each phenolic structure intercepts the nitrosation reaction, and whether the standard laboratory test used to measure this protective capacity was telling the whole truth.

To find out, the team built a simplified cured meat model built around N-acetyltryptophan, a tryptophan derivative chosen because it carries a useful light-absorbing chromophore and retains the amide bond found in covalently linked amino acids within real proteins. The model contained nitrite at 120 parts per million, matching the newly reduced industrial maximum, plus 30 micromolar of non-heme iron, a pro-oxidant naturally present in meat. The researchers then tracked the formation of N-acetyl-N-nitrosotryptophan, a model secondary N-nitrosamine, over time at two pH values: pH 5, simulating meat processing and the early stage of gastric digestion, and pH 2.5, representing the harshly acidic final stage of digestion in the stomach. Using ultra-high-performance liquid chromatography coupled to diode-array detection and ion-trap mass spectrometry, they followed not only the target nitrosamine but dozens of newly formed reaction products.

The baseline behavior of the model system was itself revealing. At pH 2.5, nitrosation of the tryptophan derivative was rapid, reaching a maximum conversion of 17.2 percent within 45 minutes, but the resulting nitrosamine proved unstable and reverted quantitatively back to its parent amine within hours through acid-catalyzed denitrosation. At pH 5, the reaction was slower and the product more persistent, with a maximum conversion of 3.6 percent. This matters because nitrosated amino acids and peptides formed in the acidic stomach could pass into the near-neutral environment of the duodenum, around pH 6.5, where they would be stabilized before intestinal absorption. In other words, the stomach is not merely a hostile environment for nitrosamines; it is a potential factory for them, and whatever survives the journey onward is the more dangerous cargo.

When the phenolic compounds entered the picture, the differences between them were striking. Caffeic acid and ferulic acid, the two unesterified hydroxycinnamic acids, were the champions, suppressing nitrosation by 85 percent within 15 minutes at pH 2.5 and achieving complete inhibition after 105 minutes. At pH 5, caffeic acid still held inhibition between 66 and 77 percent over the reaction period. Chlorogenic acid, which is simply caffeic acid esterified with quinic acid, performed markedly worse, managing only 24 percent inhibition at pH 2.5 and 16 to 28 percent at pH 5. Hydroxytyrosol fell in between. The lesson was clear and chemically elegant: the same reactive core can behave very differently depending on whether a bulky ester group blocks access to it.

The mass spectrometric detective work revealed two fundamentally different protection strategies at play. For chlorogenic acid and hydroxytyrosol, both bearing a catechol group, the story begins with nitrite-induced oxidation. Nitrite strips electrons from the catechol ring, generating a reactive quinone intermediate. That quinone can then dimerize with another phenol molecule, undergo nitration to form nitrochlorogenic acid or nitrohydroxytyrosol, or be attacked by nucleophiles. Each of these pathways consumes multiple nitrite ions; nitration of a single catechol unit alone requires three. Hydroxytyrosol proved especially voracious, scavenging at least three nitrite ions per molecule at both pH values, with nitrohydroxytyrosol emerging as its dominant product and a rich menagerie of dimers, trimers and covalent adducts with the tryptophan derivative accumulating alongside.

Caffeic and ferulic acid took an entirely different route. Instead of being oxidized, their propenoic acid side chains were directly attacked by the nitrosonium ion, the very electrophile that would otherwise nitrosate the amine. This creates a resonance-stabilized nitroso cation on the phenolic molecule, and here comes the surprise: the tryptophan derivative, present in threefold excess, turned out to be a stronger nucleophile than water or nitrite, and it covalently latched onto that cation. The result was a family of acetaldehyde oxime adducts, some still bearing the nitrosated amine, others stripped of it. In effect, caffeic and ferulic acid were acting as decoys, diverting the nitrosating machinery and then capturing the amine target itself before it could be converted into a free, mobile nitrosamine.

That capture, however, exposed a hidden flaw in the standard assay. Because the covalently bound tryptophan derivative escaped quantification, the apparent disappearance of the free amine inflated the measured antinitrosating capacity of caffeic and ferulic acid. When the researchers recalculated protection based on the number of nitrite ions actually scavenged by the five major end products of each reaction, the ranking shifted. Hydroxytyrosol emerged as superior to chlorogenic acid at pH 5, while the two catechol compounds matched each other at pH 2.5, and the unesterified hydroxycinnamic acids, despite their dazzling performance in the simple test, actually quench less nitrite per molecule. The team showed that the same bias applies to flavonoids such as rutin, quercetin and epicatechin studied previously, meaning the corrected framework offers a more honest yardstick for screening plant extracts intended for cured meat reformulation.

The practical implications reach beyond the laboratory beaker. Phenolic-rich extracts from olive, grape and rosemary have already been shown to lower volatile N-nitrosamines in sausages and bacon, and olive leaf extract rich in oleuropein, an acylated hydroxytyrosol derivative, has been tested in ripened industrial sausages as a partial nitrite replacement. The new mechanistic map explains why such extracts work and which structural features matter most: catechol groups that surrender electrons to nitrite, and free propenoic chains that intercept the nitrosonium ion directly. It also raises a nutritional angle worth savoring. Eating plant foods rich in these phenols alongside cured meats, or indeed alongside the dietary nitrate from leafy vegetables that fuels endogenous nitrite production in the stomach, could dampen the nitrosation of amino acids during digestion itself. There remain open questions, notably the toxicological significance of the structurally modified peptides released when phenols bind covalently to food proteins, but the study firmly establishes that the chemistry of protection is as intricate as the chemistry of harm, and that understanding both is the surest path to a safer plate.

Subject of Research: Inhibition of N-nitrosamine formation by plant phenolic compounds in cured meat and gastric digestion models

Article Title: The antinitrosating capacity of hydroxycinnamic acids and hydroxytyrosol in a cured meat model unraveled through structural and kinetic investigations

Article References: The antinitrosating capacity of hydroxycinnamic acids and hydroxytyrosol in a cured meat model unraveled through structural and kinetic investigations. (n.d.). https://doi.org/10.1016/j.crfs.2026.101581

Image Credits: AI Generated

DOI: 10.1016/j.crfs.2026.101581

Keywords: N-nitrosamines, nitrite, cured meat, polyphenols, hydroxytyrosol, caffeic acid, ferulic acid, chlorogenic acid, food chemistry, nitrosation, gastric digestion, food safety

The research team focused on two cultivars with very different personalities: A. tricolor L. cv. Valentina, a red-leaved variety, and A. cruentus L. cv. Krepysh, a green-leaved type. Plants were grown outdoors at the Federal Horticultural Research Center for Breeding, Agrotechnology and Nursery in Moscow across the 2020–2021 seasons, with drought imposed after two months of growth by withholding water until substrate humidity fell to 20–25 percent, a condition maintained for seven days before sampling. Ten biological and ten technical replicates per treatment gave the researchers a statistically robust foundation for comparing stressed and well-watered leaves.

What they found was a dramatic metabolic reprogramming. In the leaves of cv. Valentina, drought triggered an approximately 70-fold surge in mannonic acid, a 40-fold rise in myo-inositol, a 23-fold increase in caffeic acid, a 15-fold jump in tartaric acid, and a seven-fold elevation of glycerol. The amino acids L-proline and serine climbed four-fold, while glycolic, oxalic, and lactic acids rose two to three times. These molecules are classic osmoprotectants and compatible solutes: by accumulating inside cells, they lower osmotic potential, helping leaves retain turgor and water even as the soil dries out around their roots.

Each of these metabolites plays a distinct protective role. Myo-inositol, for instance, is far more than a simple osmolyte; it is a core precursor in the phosphoinositide signaling pathway, which mediates intracellular signal transduction and orchestrates the downstream transcriptional activation of drought-responsive genes. Caffeic acid, a key intermediate in the phenylpropanoid pathway, boosts the plant’s non-enzymatic antioxidant capacity by scavenging the reactive oxygen species that accumulate when drought inhibits photosynthesis, thereby preventing lipid peroxidation and cellular damage. Flavonoids such as apigenin add another layer of defense, neutralizing ROS and maintaining cellular redox homeostasis.

In total, the team annotated 41 distinct substances across the leaf extracts, with 40 detected in cv. Krepysh and 34 in cv. Valentina. Nine of these compounds carry documented antimicrobial properties, including lactic, pyruvic, glyoxylic, malic, acrylic, and tartaric acids, along with glycerol, acetamide, and benzoic acid. Under baseline conditions, lactic, benzoic, malic, and mannonic acids were 40, 6, 2, and 1.5 times more abundant, respectively, in cv. Valentina than in cv. Krepysh. Glyoxylic acid appeared exclusively in the green-leaved cultivar, while acetamide was unique to the red-leaved one, underscoring the distinct biochemical identities of the two varieties.

Yet the study’s most provocative contribution lies not in the biology but in the analytical chemistry. Conventional high-throughput metabolomics suffers from a sobering limitation: typically only 5 to 15 percent of the spectral features in a complex mass spectrometry dataset can be unambiguously assigned using existing database-searching algorithms. Incomplete derivatization, analyte degradation, matrix effects, and co-eluting metabolites all conspire to blur the picture. Structurally similar compounds and stereoisomers often produce virtually identical mass spectra, and library matching scores below 750 or correlation coefficients under 0.98 leave annotators guessing, with real risks of structural misidentification.

To break through this bottleneck, the authors deployed a framework they call stochastic dynamics mass spectrometry, or SD-MS. Rather than treating mass spectra as static fingerprints to be matched against libraries, SD-MS models ion fragmentation and peak formation as stochastic processes governed by the electronic structures, ground-state energies, and vibrational frequencies of isolated ionic species. The mathematical equations link experimental measurands such as mass-to-charge ratios and ion peak intensities directly to intrinsic molecular properties and three-dimensional structural parameters, explicitly accounting for the random fluctuations and signal variances that conventional deterministic models ignore.

The framework proved its mettle on notoriously difficult cases. Fumaric acid, for example, yielded a low library score of 710 that could not distinguish its E- and Z-isomers, yet SD-MS correlation analysis achieved coefficients as high as 0.9965 for the E-isomer by comparing theoretical ion intensities with experimental data. For the flavonoid apigenin, whose spectrum is nearly indistinguishable from its structural isomer genistein, the method delivered a correlation of 0.99977, clearly separating the two. Silylated dicarboxylic acids and even bulky synthetic fluorinated derivatives of trifluoroacetic acid reached correlations up to 0.99985, far exceeding the performance of standard omics-matching algorithms.

The quantum-chemical engine behind these calculations relied on density functional theory with the hybrid meta-GGA M06-2× functional and basis sets including SDD, LANL2DZ, and aug-cc-pVDZ, executed in Gaussian, Dalton, and GAMESS-US packages. Geometry optimizations, transition-state validations, and Born–Oppenheimer molecular dynamics simulations provided the theoretical ion intensities that were then cross-correlated with experimental measurements using rigorous chemometrics, including Shapiro–Wilk normality tests and two-way ANOVA to account for random error sources across scan intervals.

Beyond the technical triumph, the work carries real agricultural weight. The enriched antioxidant and nutraceutical profile of cv. Valentina, with its superior adaptive potential under water deficit, marks it as a promising genetic source for breeding programs aimed at climate-resilient crops. By identifying specific biochemical markers of drought tolerance and pairing them with an analytical tool capable of definitive three-dimensional molecular identification, the study offers both a blueprint for understanding plant resilience and a practical foundation for engineering or breeding the drought-proof vegetables of the future.

Subject of Research: Drought-induced metabolite profiling of Amaranthus tricolor and Amaranthus cruentus leaves by GC–MS and stochastic dynamics mass spectrometry

Article Title: Gas chromatography–mass spectrometry molecular structural analysis of Amaranth leaf metabolites under drought stress

Article References: Feng, J., Gins, E., Ivanova, B., Motyleva, S., Gins, V., Gins, M., & Zhang, H. (2026). Gas chromatography–mass spectrometry molecular structural analysis of Amaranth leaf metabolites under drought stress. Results in Chemistry, 30, Article 103816. https://doi.org/10.1016/j.rechem.2026.103816

Image Credits: AI Generated

DOI: 10.1016/j.rechem.2026.103816

Keywords: amaranth, drought stress, metabolomics, gas chromatography–mass spectrometry, stochastic dynamics mass spectrometry, osmoprotectants, antioxidants, myo-inositol, caffeic acid, apigenin, quantum chemistry, plant resilience