Preferential Stabilization Research Articles

Influence of Ti-incorporated Zeolite Topology and Pore Condensation on Vapor Phase Propylene Epoxidation Kinetics with Gaseous H2O2.

Vapor-phase propylene (C3H6) epoxidation kinetics with hydrogen peroxide (H2O2) strongly reflects the physical properties of Ti-incorporated zeolite catalysts and the presence of spectating molecules ("solvent") near active sites even without a bulk liquid phase. Steady-state turnover rates of C3H6 epoxidation and product selectivities vary by orders of magnitudes, depending on the zeolite silanol ((SiOH)x) density, pore topology (MFI, *BEA, FAU), and the quantity of condensed acetonitrile (CH3CN) molecules nearby active sites, under identical reaction mechanisms sharing activated H2O2 intermediates on Ti surfaces. Individual kinetic analyses for propylene oxide (PO) ring-opening, homogeneous diol oxidative cleavage, and homogeneous aldehyde oxidation reveal that secondary reaction kinetics following C3H6 epoxidation responds more sensitively to the changes in zeolite physical properties and pore condensation with CH3CN. Thus, higher PO selectivities achieved in hydrophilic Ti-MFI at steady-state reflect the preferential stabilization of transition states for C3H6 epoxidation (a primary reaction) relative to PO ring-opening and oxidative cleavage (secondary reactions) that solvation effects that reflect interactions among condensed CH3CN within pores and the extended pore structure.

Influence of Ti‐incorporated Zeolite Topology and Pore Condensation on Vapor Phase Propylene Epoxidation Kinetics with Gaseous H2O2

AbstractVapor‐phase propylene (C3H6) epoxidation kinetics with hydrogen peroxide (H2O2) strongly reflects the physical properties of Ti‐incorporated zeolite catalysts and the presence of spectating molecules (“solvent”) near active sites even without a bulk liquid phase. Steady‐state turnover rates of C3H6 epoxidation and product selectivities vary by orders of magnitudes, depending on the zeolite silanol ((SiOH)x) density, pore topology (MFI, *BEA, FAU), and the quantity of condensed acetonitrile (CH3CN) molecules nearby active sites, under identical reaction mechanisms sharing activated H2O2 intermediates on Ti surfaces. Individual kinetic analyses for propylene oxide (PO) ring‐opening, homogeneous diol oxidative cleavage, and homogeneous aldehyde oxidation reveal that secondary reaction kinetics following C3H6 epoxidation responds more sensitively to the changes in zeolite physical properties and pore condensation with CH3CN. Thus, higher PO selectivities achieved in hydrophilic Ti‐MFI at steady‐state reflect the preferential stabilization of transition states for C3H6 epoxidation (a primary reaction) relative to PO ring‐opening and oxidative cleavage (secondary reactions) that solvation effects that reflect interactions among condensed CH3CN within pores and the extended pore structure.

Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking.

Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and machine-learning-based binding pocket detection with the ensemble-based ligand docking and binding free energy analysis to characterize the potential allosteric binding sites and determine structural and energetic determinants of allosteric inhibition for a series of experimentally validated allosteric molecules. The results demonstrate a good agreement between computational and experimental binding affinities, providing support to the predicted binding modes and suggesting key interactions formed by the allosteric ligands to elicit the experimentally observed inhibition. We establish structural and energetic determinants of allosteric binding for the experimentally known allosteric molecules, indicating a potential mechanism of allosteric modulation by targeting the hinges of the inter-protomer movements and blocking conformational changes between the closed and open spike trimer forms. The results of this study demonstrate that combining ensemble-based ligand docking with conformational states of spike protein and rigorous binding energy analysis enables robust characterization of the ligand binding modes, the identification of allosteric binding hotspots, and the prediction of binding affinities for validated allosteric modulators, which is consistent with the experimental data. This study suggested that the conformational adaptability of the protein allosteric sites and the diversity of ligand bound conformations are both in play to enable efficient targeting of allosteric binding sites and interfere with the conformational changes.

The binding and mechanism of a positive allosteric modulator of Kv3 channels

Small-molecule modulators of diverse voltage-gated K+ (Kv) channels may help treat a wide range of neurological disorders. However, developing effective modulators requires understanding of their mechanism of action. We apply an orthogonal approach to elucidate the mechanism of action of an imidazolidinedione derivative (AUT5), a highly selective positive allosteric modulator of Kv3.1 and Kv3.2 channels. AUT5 modulation involves positive cooperativity and preferential stabilization of the open state. The cryo-EM structure of the Kv3.1/AUT5 complex at a resolution of 2.5 Å reveals four equivalent AUT5 binding sites at the extracellular inter-subunit interface between the voltage-sensing and pore domains of the channel’s tetrameric assembly. Furthermore, we show that the unique extracellular turret regions of Kv3.1 and Kv3.2 essentially govern the selective positive modulation by AUT5. High-resolution apo and bound structures of Kv3.1 demonstrate how AUT5 binding promotes turret rearrangements and interactions with the voltage-sensing domain to favor the open conformation.

Site-selective protonation enables efficient carbon monoxide electroreduction to acetate

Electrosynthesis of acetate from CO offers the prospect of a low-carbon-intensity route to this valuable chemical––but only once sufficient selectivity, reaction rate and stability are realized. It is a high priority to achieve the protonation of the relevant intermediates in a controlled fashion, and to achieve this while suppressing the competing hydrogen evolution reaction (HER) and while steering multicarbon (C2+) products to a single valuable product––an example of which is acetate. Here we report interface engineering to achieve solid/liquid/gas triple-phase interface regulation, and we find that it leads to site-selective protonation of intermediates and the preferential stabilization of the ketene intermediates: this, we find, leads to improved selectivity and energy efficiency toward acetate. Once we further tune the catalyst composition and also optimize for interfacial water management, we achieve a cadmium-copper catalyst that shows an acetate Faradaic efficiency (FE) of 75% with ultralow HER (<0.2% H2 FE) at 150 mA cm−2. We develop a high-pressure membrane electrode assembly system to increase CO coverage by controlling gas reactant distribution and achieve 86% acetate FE simultaneous with an acetate full-cell energy efficiency (EE) of 32%, the highest energy efficiency reported in direct acetate electrosynthesis.

In vivo determination of analgesic and anti-inflammatory activities of isolated compounds from Cleome amblyocarpa and molecular modelling for the top active investigated compounds.

Cleome amblyocarpa Barr. and Murb. from the family Cleomaceae is used in folk medicine as it has analgesic, anti-inflammatory, antibacterial and antioxidant activities. In this study, ten compounds from the whole plant of C. amblyocarpa, a wild plant that grows in the Sinai Peninsula of Egypt, were isolated. Six compounds, β-sitosterol 3-O-β-d-glucoside 2, calycopterin 5, rhamnocitrin 6, 17α-hydroxycabraleahy-droxylactone 7, cleogynol 8, and β-sitosterol 10 were first isolated from this species. In addition, four previously reported compounds, kaempferol-3, 7-dirhamnoside 1, 15α-acetoxycleomblynol A 3, and 11-α-acetylbrachy-carpone-22(23)-ene 4, as well as cleocarpanol 9, were isolated and identified. Isolated compounds were evaluated to determine their analgesic properties utilizing a hot-plate test method, and their anti-inflammatory effects utilizing rat paw edema. In a hot-plate test, compounds 3, 4, 7, 8, and 9 showed significant pain inhibition in latency time as compared to the normal group. Compounds 3-9 exhibited a significant inhibition of carrageenan-induced inflammation. According to the results of this work, compounds 3 and 4 (Dammarane triterpenoid) have the strongest analgesic/anti-inflammatory activity as compared to the other tested compounds. These results give support to the medicinal benefits of the plant as an analgesic along with an anti-inflammatory agent in traditional therapy. Molecular modelling studies of the isolated compounds 3 and 4 assessed the molecular affinity and binding interaction patterns for these compounds towards COX-2 as compared to specific COX-2 inhibitors and in relation to COX-1 isozyme. Compound 3 revealed extended accommodation across COX-2's hydrophobic sub-pockets and preferential thermodynamic stability across molecular dynamics simulations.

Enhanced oral delivery of hesperidin-loaded sulfobutylether-β-cyclodextrin/chitosan nanoparticles for augmenting its hypoglycemic activity: in vitro-in vivo assessment study

Hesperidin (Hsd), a bioactive phytomedicine, experienced an antidiabetic activity versus both Type 1 and Type 2 Diabetes mellitus. However, its intrinsic poor solubility and bioavailability is a key challenging obstacle reflecting its oral delivery. From such perspective, the purpose of the current study was to prepare and evaluate Hsd-loaded sulfobutylether-β-cyclodextrin/chitosan nanoparticles (Hsd/CD/CS NPs) for improving the hypoglycemic activity of the orally administered Hsd. Hsd was first complexed with sulfobutylether-β-cyclodextrin (SBE-β-CD) and the complex (CX) was found to be formed with percent complexation efficiency and percent process efficiency of 50.53 ± 1.46 and 84.52 ± 3.16%, respectively. Also, solid state characterization of the complex ensured the inclusion of Hsd inside the cavity of SBE-β-CD. Then, Hsd/CD/CS NPs were prepared using the ionic gelation technique. The prepared NPs were fully characterized to select the most promising one (F1) with a homogenous particle size of 455.7 ± 9.04 nm, a positive zeta potential of + 32.28 ± 1.12 mV, and an entrapment efficiency of 77.46 ± 0.39%. The optimal formula (F1) was subjected to further investigation of in vitro release, ex vivo intestinal permeation, stability, cytotoxicity, and in vivo hypoglycemic activity. The results of the release and permeation studies of F1 manifested a modulated pattern between Hsd and CX. The preferential stability of F1 was observed at 4 ± 1 °C. Also, the biocompatibility of F1 with oral epithelial cell line (OEC) was retained up to a concentration of 100 µg/mL. After oral administration of F1, a noteworthy synergistic hypoglycemic effect was recorded with decreased blood glucose level until the end of the experiment. In conclusion, Hsd/CD/CS NPs could be regarded as a hopeful oral delivery system of Hsd with enhanced antidiabetic activity.Graphical

Enhancing densification rate and the unusual 4H-SiC polytype stabilization in ultrafast high-temperature sintering of α-SiC

Novel Powder medium-based Ultrafast High-temperature Sintering (P-UHS) technique brings unexplored opportunities for the ultrarapid consolidation of large-sized and difficult-to-sinter ceramics with a complex shape. Herein, the P-UHS was demonstrated to be very effective means for the densification of large-sized α-SiC bulks (∼16 cm3) with boron and carbon additions under heating rates exceeding 1500 °C/min. Bulk ceramics with ∼97% density and homogenous microstructure were obtained within only 6 min. The ultrafast heating led to two orders of magnitude increase in the densification rate contributing to an energy saving of 90% if compared to conventional sintering process. In addition, the preferential 4H-SiC polytype stabilization was observed only when ultrafast heating rate was employed. The non-equilibrium transient chemistry and the ultrarapid shrinkage were considered as the major drivers for this unusual phenomenon.

Nanosized antiferromagnetic domains in NiO/Ag(001) films probed by polarised X-ray and unpolarised low-energy electrons

Surface antiferromagnetism of NiO film, epitaxially deposited on Ag(001), is investigated using the absorption of linearly polarised X-ray and the diffraction of low-energy unpolarised electrons. Polarisation-dependent X-ray absorption studies reveal a preferential stabilisation of the magnetic domains with the main components of magnetic axes parallel to the interface. Furthermore, the role of interfacial strain-induced magnetocrystalline anisotropy below a critical film thickness (∼ 20 ML) could be demonstrated by the magnetic linear dichroism results. Utilising the exchange scattered electrons from various antiferromagnetic (111) planes, the magnetic twin domains could be probed by a low energy electron microscope operating in the dark-field mode. The linearly polarised X-ray, on the other hand, is sensitive to the magnetic axes orientations of Ni2+ ions and therefore, provides access to the spin domains as well as the twin domains. Comparison of results of these two independent imaging techniques demonstrates that the in-plane component of the magnetic easy axes contained by the complementary T-domains are parallel to each other.

Impact of Mg on Pd-based methane oxidation catalysts for lean-burn natural gas emissions control

More efficient lean-burn, natural gas engines are limited by greenhouse gas emissions due to methane oxidation catalysts (MOC) that suffer from water inhibition and high temperature activation. Herein, we report that the addition of Mg to supported 1 wt% Pd MOCs improved hydrothermal stability even after severe hydrothermal aging. The superior methane oxidation activity compared to the corresponding Mg-free catalyst was attributed to (1) influence of Mg during surface roughening and restructuring at 700 °C on metal-support interaction, (2) reducibility of PdOx sites and (3) preferential stabilization of active Pd (1 0 0) facets in the sample as was evidenced by H2 TPR and CO TPD characterization experiments. Methane conversion under synthetic exhaust conditions relevant to natural gas, lean-burn engines were investigated. BET, TPR, CO pulse chemisorption followed by TPD provided valuable insights into the surface area, pore volume, reducibility, Pd dispersion and Pd particle size of the selected catalyst samples.

“Structural and NIR photoluminescence studies from Nd3+-doped yttrium niobate: A potential material for photonics”

In the present work, an original sol-gel methodology is explored for the synthesis of Nd3+-doped yttrium niobate materials. The main goal was to assess the effect of the dopant concentration on the structural and luminescent properties, specifically in the near-infrared region, aiming for a future biophotonics application. X-ray diffraction and Raman spectroscopy analyses revealed the crystallization of the cubic Y3NbO7 and monoclinic YNbO4 phases, with preferential stabilization of the cubic Y3NbO7, a fluorite-like structure, irrespective of the dopant concentration. All samples presented an intense NIR emission in the second biological window (1000–1500 nm) under excitation at 808 nm (NIR–I excitation), with a prevalence for the 1064 nm emission, indicating the potential application in the biophotonics field. Up to 5 mol% Nd3+ content did not modify the spectral profiles, and the lifetime decay for the 4F3/2 emission level showed that the quenching concentration was 1.78 mol% Nd3+. Higher Nd3+ content revealed broader emission bands, attributed to higher occupation of Y3NbO7 symmetry sites. Emission at NIR-IIa biological window, at 1336 nm, attributed to the 4F3/2 → 4I13/2 was detected indicating the distribution of Nd3+ ions in a low phonon energy environment. The as-reported materials reveal potential application as solid-state lasers and bioimaging probes at NIR-IIa biological window.

Preferential recruitment and stabilization of Myosin II at compartment boundaries in Drosophila.

The regulation of mechanical tension exerted at cell junctions guides cell behavior during tissue formation and homeostasis. Cell junctions along compartment boundaries, which are lineage restrictions separating cells with different fates and functions within tissues, are characterized by increased mechanical tension compared to that of cell junctions in the bulk of the tissue. Mechanical tension depends on the actomyosin cytoskeleton; however, the mechanisms by which mechanical tension is locally increased at cell junctions along compartment boundaries remain elusive. Here, we show that non-muscle Myosin II and F-actin transiently accumulate and mechanical tension is increased at cell junctions along the forming anteroposterior compartment boundary in the Drosophila melanogaster pupal abdominal epidermis. Fluorescence recovery after photobleaching experiments showed that Myosin II accumulation correlated with its increased stabilization at these junctions. Moreover, photoconversion experiments indicated that Myosin II is preferentially recruited within cells to junctions along the compartment boundary. Our results indicate that the preferential recruitment and stabilization of Myosin II contribute to the initial build-up of mechanical tension at compartment boundaries.

Solution NMR studies reveal novel CLIC4 chaperone activity with respect to profilin-1.

Despite its name, chloride intracellular channel 4 (CLIC4) is a soluble enzyme that can catalyze glutathione-dependent thiol transfers. It is unclear how this enzymatic activity relates to its biological role in remodeling the actin cytoskeleton. Previous studies have shown that CLIC4 interacts with profilin-1, a critical regulator of actin polymerization. We confirmed a direct interaction, 170 ± 20 μM by microscale thermophoresis. However, using solution nuclear magnetic resonance (NMR) spectroscopy, we demonstrate that CLIC4 has a higher affinity for profilin when it is unfolded. Amide hydrogen exchange studies demonstrate that the N- and C-terminal helices of profilin readily unfold, whereas the central β-beta sheet core remains relatively intact. Interaction with CLIC4 increases amide exchange rates throughout profilin, indicating preferential stabilization of partially unfolded intermediates. We note that profilin is glutathionylated in proteomic studies of cells exposed to oxidative stress. Profilin is unfolded by glutathionylation of buried cysteine residues in its N- or C-terminal helices, and this disrupts its ability to bind actin, as measured by pyrene-actin polymerization assay. We are currently attempting to demonstrate that CLIC4 can reverse glutathionylation of profilin-1 and promote its refolding in cells and in vitro.

The influence of N⋯π pnicogen bonding in π-stacked parallel displaced geometry of nitrobenzene dimers: Evidence using matrix isolation infrared spectroscopy and ab initio computations

The present study elucidates the preferential stabilization of parallel displaced geometry of nitrobenzene dimers by co-operative action of π…π interactions and ON⋯π pnicogen bonding. The homodimers have also been synthesized within Ne and Ar matrixes at cryogenic temperatures followed by their characterization using infrared spectroscopy. The significant contribution of short-range dispersion forces in stabilization of parallel-displaced geometries causes a concomitant rise in Pauli repulsion effects, owing to increased electron correlation. This destabilization is efficiently compensated for, by the added electrostatic effects due to the π-hole facilitated ON⋯π pnicogen bond. The directional determinism of the pnicogen bond proves pivotal in facilitating this co-operation with π…π interactions. These inferences have been obtained by a comparative computational analysis of the parallel displaced and ‘T-shaped’ geometries of the benzene homodimer, with their nitrobenzene analogues.

Molecular insights into the stereospecificity of arginine in RNA tetraloop folding.

One of the hypotheses for the homochirality of amino acids in the context of the origin of life is that only a particular stereoisomer provides preferential stability to RNA folding by acting as a chemical chaperon. However, the effect at the molecular level is not well understood. This study provides a molecular understanding of such preferential stability for a small GAAA RNA tetraloop in the presence of chiral arginine through a multidimensional free energy landscape constructed using a combination of umbrella sampling and parallel bias metadynamics (PBMetaD) simulations. We show that the origin of the chirality difference in RNA folding-unfolding dynamics is due to differences in the configurational diversity of RNA in adopting various non-natural conformations that accompany the diverse binding modes of D-arginine and L-arginine. We show that while D-arginine stabilizes the native folded state of RNA, L-arginine destabilizes it. Furthermore, free energy calculations on the binding of D- and L-arginine reveal a specific geometric constraint that helps D-arginine to stack with the terminal base pairs of RNA and pushes L-arginine for groove binding.

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Preferential stabilization of c-MYC and BCL-2 promoter G-quadruplexes by a natural betaine-type alkaloid

In this study, we demonstrate for the first time that the betaine-type alkaloid Lycobetaine ( LYC ) preferentially binds to c-MYC and BCL-2 promoter G-quadruplexes (G4s). Biophysical experiments including absorption titrations, CD melting and NMR studies showed that LYC had the ability to bind and stabilize both c-MYC and BCL-2 G4s through an end-stacking mode. Additional biological assays including RT-PCR and Western blotting indicated that LYC simultaneously inhibited the expression of c-MYC and BCL-2 oncogenes in A549/DDP cells, which thereby led to cell cycle arrest, apoptosis, as well as inhibition on cell proliferation and migration. Taken together, these results revealed a new potential anticancer mechanism of LYC with potential application of LYC in drug-resistant cancers. • The betaine-type alkaloid lycobetaine ( LYC ) preferentially binds to c-MYC and BCL-2 promoter G-quadruplexes. • LYC simultaneously inhibits the expression of c-MYC and BCL-2 oncogenes. • This study uncovers a new potential anticancer mechanism of LYC . • This work extended the application of LYC in drug-resistant cancers.

How to Stabilize Carbenes in Enzyme Active Sites without Metal Ions.

Carbenes are highly reactive compounds with unique value to synthetic chemistry. However, a small number of natural enzymes have been shown to utilize carbene chemistry, and artificial enzymes engineered with directed evolution required transition metal ions to stabilize the carbene intermediates. To facilitate the design of broader classes of enzymes that can take advantage of the rich carbene chemistry, it is thus important to better understand how to stabilize carbene species in enzyme active sites without metal ions. Motivated by our recent studies of the anaerobic ergothioneine biosynthesis enzyme EanB, we examine carbene-protein interaction with both cluster models and QM/MM simulations. The cluster calculations find that an N-heterocyclic carbene interacts strongly with polar and positively charged protein motifs. In particular, the interaction between a guanidinium group and carbene is as strong as ∼30 kcal/mol, making arginine a great choice for the preferential stabilization of carbenes. We also compare the WT EanB and its mutant in which the key tyrosine was replaced by a non-natural analogue (F2Tyr) using DFTB3/MM simulations. The calculations suggest that the carbene intermediate in the F2Tyr mutant is more stable than that in the WT enzyme by ∼3.5 kcal/mol, due to active site rearrangements that enable a nearby arginine to better stabilize the carbene in the mutant. Overall, the current work lays the foundation for the pursuit of enzyme designs that can take advantage of the unique chemistry offered by carbenes without the requirement of metal ions.

Targeting Parallel Topology of G-Quadruplex Structures by Indole- Fused Quindoline Scaffolds.

Preferential stabilization of G-quadruplex (G4) structures using small-molecule ligands has emerged as an effective approach to develop anticancer drugs. Herein, we report the synthesis of three indole-fused quindoline derivatives with varying lengths of side chains (InqEt1, InqEt2, and InqPr2) as selective ligands for promoter G4 structures. The ligands stabilize the parallel topology of c-MYC and c-KIT1 promoter G4 DNAs over telomeric and duplex DNAs, as evident from the circular dichroism melting and polymerase stop-assay experiments. The lead ligand, InqPr2, downregulates the gene expression of c-MYC and c-KIT in HeLa and HepG2 cells, respectively, leading to apoptotic cell death. Molecular modeling and dynamics studies support the 2:1 binding stoichiometry revealed from the Job plot analysis and show the ligand's structural features that enable the preferential binding to the parallel G4 structures over other topologies. Our studies show that indole-fused quindoline derivatives can be harnessed as new molecular scaffolds for selective targeting of parallel G4 topologies.

Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics.

Since the emergence of the pandemic of the coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the discovery of antiviral phytoconstituents from medicinal plants against SARS-CoV-2 has been comprehensively researched. In this study, thirty-three plants belonging to seventeen different families used traditionally in Saudi Arabia were tested in vitro for their ability to inhibit the SARS-CoV-2 main protease (MPRO). Major constituents of the bio-active extracts were isolated and tested for their inhibition potential against this enzyme; in addition, their antiviral activity against the SARS-CoV-2 Egyptian strain was assessed. Further, the thermodynamic stability of the best active compounds was studied through focused comparative insights for the active metabolites regarding ligand–target binding characteristics at the molecular level. Additionally, the obtained computational findings provided useful directions for future drug optimization and development. The results revealed that Psiadia punctulata, Aframomum melegueta, and Nigella sativa extracts showed a high percentage of inhibition of 66.4, 58.7, and 31.5%, against SARS-CoV-2 MPRO, respectively. The major isolated constituents of these plants were identified as gardenins A and B (from P. punctulata), 6-gingerol and 6-paradol (from A. melegueta), and thymoquinone (from N. sativa). These compounds are the first to be tested invitro against SARS-CoV-2 MPRO. Among the isolated compounds, only thymoquinone (THY), gardenin A (GDA), 6-gingerol (GNG), and 6-paradol (PAD) inhibited the SARS-CoV-2 MPRO enzyme with inhibition percentages of 63.21, 73.80, 65.2, and 71.8%, respectively. In vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020 (accession number on GSAID: EPI_ISL_430820) revealed a strong-to-low antiviral activity of the isolated compounds. THY showed relatively high cytotoxicity and was anti-SARS-CoV-2, while PAD demonstrated a cytotoxic effect on the tested VERO cells with a selectivity index of CC50/IC50 = 1.33 and CC50/IC50 = 0.6, respectively. Moreover, GNG had moderate activity at non-cytotoxic concentrations in vitro with a selectivity index of CC50/IC50 = 101.3/43.45 = 2.3. Meanwhile, GDA showed weak activity with a selectivity index of CC50/IC50 = 246.5/83.77 = 2.9. The thermodynamic stability of top-active compounds revealed preferential stability and SARS-CoV-2 MPRO binding affinity for PAD through molecular-docking-coupled molecular dynamics simulation. The obtained results suggest the treating potential of these plants and/or their active metabolites for COVID-19. However, further in-vivo and clinical investigations are required to establish the potential preventive and treatment effectiveness of these plants and/or their bio-active compounds in COVID-19.