Thermodynamics Of Binding Research Articles

Biophysical characterization of blood coagulation factor VIII binding to lipid nanodiscs that mimic activated platelet surfaces.

Following proteolytic activation, activated blood coagulation factor VIII (FVIIIa) binds to activated platelet membranes, forming the intrinsic tenase complex with activated factor IX (FIXa). Previous studies have identified the C1 and C2 domains as the membrane binding domains of FVIII through conserved arginine residues. A membrane binding model for the FVIII C domains proposes that surface exposed hydrophobic and positively charged residues at each C domain interact with the membrane, yet a comprehensive thermodynamic and structural description of this interaction is lacking. To determine residues of interaction, thermodynamics, and membrane binding preference for FVIII membrane association. Binding of FVIII constructs to lipid nanodiscs were characterized with nuclear magnetic resonance (NMR), isothermal titration calorimetry (ITC), bio-layer interferometry (BLI), and X-ray crystallography. The thermodynamics of FVIII membrane binding indicate that the C1 domain associates through an enthalpically driven process while the C2 domain is entropically driven. Alanine mutations to surface-exposed hydrophobic residues in the C2 domain reveal differential effects on membrane binding, highlighting important determinants at the residue-level. The structure of a C2 double mutant, L2251A/L2252A, demonstrates that its decreased affinity is likely due to decreasing the surface area hydrophobicity. NMR studies with the C2 domain identified residues of interaction with soluble O-phospho-L-serine (OPLS) as well as lipid nanodiscs. Lastly, increasing phosphatidylethanolamine (PE) and decreasing PS content decreases overall FVIII affinity for membrane surfaces. This study provides further insight into the molecular basis for how FVIII interacts with platelets to form the intrinsic tenase complex.

Crystal structure of the HMGA AT-hook 1 domain bound to the minor groove of AT-rich DNA and inhibition by antikinetoplastid drugs

High mobility group (HMG) proteins are intrinsically disordered nuclear non-histone chromosomal proteins that play an essential role in many biological processes by regulating the expression of numerous genes in eukaryote cells. HMGA proteins contain three DNA binding motifs, the “AT-hooks”, that bind preferentially to AT-rich sequences in the minor groove of B-form DNA. Understanding the interactions of AT-hook domains with DNA is very relevant from a medical point of view because HMGA proteins are involved in different conditions including cancer and parasitic diseases. We present here the first crystal structure (1.40 Å resolution) of the HMGA AT-hook 1 domain, bound to the minor groove of AT-rich DNA. In contrast to AT-hook 3 which bends DNA and shows a larger minor groove widening, AT-hook 1 binds neighbouring DNA molecules and displays moderate widening of DNA upon binding. The binding affinity and thermodynamics of binding were studied in solution with surface plasmon resonance (SPR)-biosensor and isothermal titration calorimetry (ITC) experiments. AT-hook 1 forms an entropy-driven 2:1 complex with (TTAA)2-containing DNA with relatively slow kinetics of association/dissociation. We show that N-phenylbenzamide-derived antikinetoplastid compounds (1–3) bind strongly and specifically to the minor groove of AT-DNA and compete with AT-hook 1 for binding. The central core of the molecule is the basis for the observed sequence selectivity of these compounds. These findings provide clues regarding a possible mode of action of DNA minor groove binding compounds that are relevant to major neglected tropical diseases such as leishmaniasis and trypanosomiasis.

Thermodynamics of Anion Binding by (Thio)ureido-calix[4]arene Derivatives in Acetonitrile

Thermodynamics of Anion Binding by (Thio)ureido-calix[4]arene Derivatives in Acetonitrile

Thermodynamics of Magnesium Binding at Calcite Kink Sites and Implications for Growth inhibition

Thermodynamics of Magnesium Binding at Calcite Kink Sites and Implications for Growth inhibition

Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features

The non-ideal accuracy and insufficient selectivity of CRISPR/Cas9 systems is a serious problem for their use as a genome editing tool. It is important to select the target sequence correctly so that the CRISPR/Cas9 system does not cut similar sequences. This requires an understanding of how and why mismatches in the target sequence can affect the efficiency of the Cas9/sgRNA complex. In this work, we studied the catalytic activity of the Cas9 enzyme to cleave DNA substrates containing nucleotide mismatch at different positions relative to the PAM in the “seed” sequence. We show that mismatches in the complementarity of the sgRNA/DNA duplex at different positions relative to the protospacer adjacent motif (PAM) sequence tend to decrease the cleavage efficiency and increase the half-maximal reaction time. However, for two mismatches at positions 11 and 20 relative to the PAM, an increase in cleavage efficiency was observed, both with and without an increase in half-reaction time. Thermodynamic parameters were obtained from molecular dynamics results, which showed that mismatches at positions 8, 11, and 20 relative to the PAM thermodynamically stabilize the formed complex, and a mismatch at position 2 of the PAM fragment exerts the greatest stabilization compared to the original DNA sequence. The weak correlation of the thermodynamic binding parameters of the components of the Cas9/sgRNA:dsDNA complex with the cleavage data of DNA substrates containing mismatches indicates that the efficiency of Cas9 operation is mainly affected by the conformational changes in Cas9 and the mutual arrangement of sgRNA and substrates.

Proanthocyanidin Regulates NETosis and Inhibits the Growth and Proliferation of Liver Cancer Cells - In Vivo, In Vitro and In Silico Investigation.

Liver cancer ranks third in global cancer-related mortality, with about 700,000 deaths recorded yearly, making it one of the most common cancers worldwide. Even though prognoses differ according to the severity of the diseases, many patients now exhibit an increased life cycle since the implementation of chemotherapy. In the current study, we investigated the effect of proanthocyanidin ‒a polyphenol molecule found in many plants‒ on the proliferation and invasion of liver cancer cells. In particular, we determined the effect of proanthocyanidin on the serum levels of four strategic liver cancer target, TNFα, IL-6, cfDNA, and IL-1β. Further molecular insight on the inhibitory mechanism of proanthocyanidin against TNFα, IL-6, and IL-1β was obtained via molecular docking, molecular dynamics simulations and binding free energy calculations. Results showed that proanthocyanidin inhibited the growth of HepG2 and HEP3B cells, and effectively reduced clonogenic survival and invasion potential when compared to control cells. Proanthocyanidin was also found to suppress the expression of Bcl-2 (26 kDa) protein in HepG2 cells, while increasing the expression of Bax (21 kDa). Molecular dynamics (MD) and thermodynamic binding free energy calculations showed that proanthocyanidin maintained stable binding within the active site of target proteins across the entire 100 ns MD simulation period, and its binding affinity outscored respective control molecules.In conclusion, the multifaceted analysis showcased in this study demonstrated promising anti-cancer effect of proanthocyanidin on HepG2 and HEP3B cancer cells, highlighting its potential as a viable liver cancer therapeutic alternative.

Effect of Cyclodextrins Formulated in Liposomes and Gold and Selenium Nanoparticles on siRNA Stability in Cell Culture Medium

Background: Encapsulation of siRNA fragments inside liposome vesicles has emerged as an effective method for delivering siRNAs in vitro and in vivo. However, the liposome’s fluid-phospholipid bilayer of liposomes allows siRNA fragments to diffuse out of the liposome, decreasing the dose concentration and therefore the effectiveness of the carrier. We have previously reported that β-cyclodextrins formulated in liposomes help increase the stability of siRNAs in cell culture medium. Here, we continued that study to include α, γ, methyl-β-cyclodextrins and β-cyclodextrin-modified gold and selenium nanoparticles. Methods: We used Isothermal Titration Calorimetry to study the binding thermodynamics of siRNAs to the cyclodextrin-modified nanoparticles and to screen for the best adamantane derivative to modify the siRNA fragments, and we used gel electrophoresis to study the stabilization effect of siRNA by cyclodextrins and the nanoparticles. Results: We found that only β- and methyl-β-cyclodextrins increased siRNA serum stability. Cyclodextrin-modified selenium nanoparticles also stabilize siRNA fragments in serum, and siRNAs chemically modified with an adamantane moiety (which forms inclusion complexes with the cyclodextrin-modified-nanoparticles) show a strong stabilization effect. Conclusions: β-cyclodextrins are good additives to stabilize siRNA in cell culture medium, and the thermodynamic data we generated of the interaction between cyclodextrins and adamantane analogs (widely used in drug delivery studies), should serve as a guide for future studies where cyclodextrins are sought for the delivery and solvation of small organic molecules.

Preparation of pure phase silver nanoparticles: Morphological, optical, binding interactions with bovine serum albumin and antioxidant potential studies

Pure silver nanoparticles (AgNPs) were synthesized using Senecio madagascariensis plant extract and oleic acid as capping agents. The powder X-ray diffraction patterns of the silver nanoparticles were indexed to the face-centred cubic phase of Ag. TEM images of the nanoparticles revealed polydisperse spherical nanoparticles with particle size of 9 to 22 nm range. The GC-MS revealed terpenes as some phytochemicals extracted, which the FTIR bands corroborated. The results confirmed that increase in oleic acid concentration increased the size of the silver nanoparticles. The nanoparticles' optical band gaps, Eg, were 2.26 – 2.56 eV, which decreased with particle size. The AgNPs exhibited potential antioxidant activity, as demonstrated by the DPPH scavenging assay. The DPPH scavenging activity was highest, with AgNP1 at 80 % and an IC50 of 1.668 μg/mL. Fluorescence and ultraviolet (UV) titrations were used to study the interaction of the silver nanoparticles (AgNP1) with bovine serum albumin (BSA). The Kapp value of the AgNP1 was calculated to be 3.14 × 104 ± 0.02 Lmol−1, KSV calculated as 7.38 × 104 ± 0.12 M−1. In the study, AgNPs bind to BSA potentially through a static quenching mechanism with one binding site that leads to developing a ground state complex. It is proposed that AgNPs bond to BSA's surface spontaneously based on its thermodynamic characteristics and binding constants.

Purification and structural analysis of β-glucosidase from Lactobacillus acidophilus GIM1.208 and its interaction with rosamultin in Rosa roxburghii Tratt

Lactobacillus acidophilus GIM1.208 (LA) β-glucosidase (BGL) converts glycosides from Rosa roxburghii Tratt (RRT) to release more active aglycones. This study purified LA BGL and investigated it interaction with rosamultin in RRT. The isolated and purified BGL in the study had higher purity and activity, and the proportion of ordered structure in its secondary structure was greater than 60%, indicating better structural stability. The hydrolysis of purified BGL hydrolyzed rosamultin to tormentic acid at a rate of 25.2% (p < 0.01), and the hypoglycemic activity of tormentic acid was higher than that of rosamultin. Rosamultin causes BGL to undergo massive aggregation and enhances the hydrogen bonding network structure. Thermodynamic analyses indicate that their binding is a non-spontaneous exothermic entropy-decreasing reaction, with the main forces being hydrogen bonding, van der Waals forces, or protonation forces. Additionally, their thermodynamic binding constant Kd = 2.976 × 10−5 mol/L and dissociation constant KD = 2.67 × 10−5 mol/L indicate that the two have high affinity and strong interaction. In conclusion, BGL has the ability to hydrolyze rosamultin to release tormentic acid and they have a strong interaction. The results of this study can provide a reference for the study of glycoside changes and their interactions in RRT fermented by LA.

Generating globin-like reactivities in [human serum albumin-FeII(heme)] complex through N-donor ligand addition

Human serum albumin (HSA) has a strong binding affinity for heme b, forming a complex in a 1:1 ratio with the co-factor ([HSA-FeIIIheme]). This system displays spectroscopic and functional properties comparable to globins when chemical derivatives mimicking them are incorporated into the protein matrix. The aim of this study is to generate globin-like systems using [HSA-FeIIIheme] as a protein template and binding N-donor ligands (imidazole, Im; and 1-methylimidazole, 1-MeIm) to construct artificial [HSA-Fe(heme)-(N-donor)] complexes. Their electronic structure and binding thermodynamics are investigated using UV–vis and (synchronous) fluorescence spectroscopies, while ligand-protein interactions are visualized using docking simulations. The imidazole derivatives have a strong affinity for [HSA-FeIIIheme] (K ~ 104–106), where the spontaneous binding of Im and 1-MeIm are dominated by entropic and enthalpic effects, respectively. The reduced form of the [HSA-Fe(heme)-(N-donor)] complexes demonstrate nitrite reductase (NiR) activity similar to that observed in globins, but with significant differences in their rates. [HSA-FeIIheme-(1-MeIm)] reduces nitrite ~4× faster than the Im analogue, and ~ 30× faster than myoglobin (Mb). The enhanced NiR activity of [HSA-FeIIheme-(1-MeIm)] is a cumulative effect of several factors including a slightly expanded and more optimal heme binding pocket, nearby residues as possible proton sources, and a H-bonding interaction between 1-MeIm and residues Arg160 and Lys181 that may have a long-distance influence on the heme π electron density.

The Spatial Distribution of Lipophilic Cations in Gradient Copolymers Regulates Polymer-pDNA Complexation, Polyplex Aggregation, and Intracellular pDNA Delivery.

Here, we demonstrate that the spatial distribution of lipophilic cations governs the complexation pathways, serum stability, and biological performance of polymer-pDNA complexes (polyplexes). Previous research focused on block/statistical copolymers, whereas gradient copolymers, where the density of lipophilic cations diminishes (gradually or steeply) along polymer backbones, remain underexplored. We engineered gradient copolymers that combine the polyplex colloidal stability of block copolymers with the transfection efficiency of statistical copolymers. We synthesized length- and compositionally equivalent gradient copolymers (G1-G3) along with statistical (S) and block (B) copolymers of 2-(diisopropylamino)ethyl methacrylate and 2-hydroxyethyl methacrylate. We mapped how polymer microstructure governs pDNA loading per polyplex, pDNA conformational changes, and polymer-pDNA binding thermodynamics via static light scattering, circular dichroism spectroscopy, and isothermal titration calorimetry, respectively. While gradient steepness is a powerful design handle to improve polyplex physical properties, augment pDNA delivery capacity, and attenuate polycation-triggered hemolysis, microstructural contrasts did not elicit differences in complement activation.

Transglutaminase–mucin binding dynamics in gastrointestinal mucus: Interfacial behaviour, thermodynamics and gelation mechanism

Transglutaminase, an enzyme present in epithelial cells and as a residual component in processed foods, is hypothesised to interact with gastrointestinal mucus, impacting its structure and function. To test the physical validity of this phenomenon, this study investigates the binding kinetics and thermodynamics between porcine gastric mucin (PGM) and microbial transglumatinse (TGM) in a model gastrointestinal mucus, followed by the rheological analysis of the resulting systems. At pH 7, TGM exhibited pronounced binding with the PGM interface, characterised by a high surface density (55.34 ± 1.86 µg/m−2) and a low dissociation constant (KD ∼ 4.03 ± 0.10 μM) as determined by surface plasma resonance (SPR). Conversely, at pH 3, TGM showed weak adhesion onto PGM, resulting in a less stable binding, reflected by a lower surface density (10.94 ± 0.67 µg/m−2) and a higher dissociation constant (KD ∼ 6.24 ± 0.22 μM). Regardless of the nature of interaction, the Hill coefficients (nH ≥ 1) indicated that the binding sites were markedly denser at pH 7 (1383.38 ± 46.47 pmol/m−2), than at pH 3 (273.68 ± 16.84 pmol/m−2). Fluorimetry analysis suggested temperature-dependent dynamic binding between PGM and TGM. The resulting Benesi – Hildebrand plots illustrated a linear correlation between PGM and increasing TGM concentration, suggesting a single-step interaction mechanism. The calculated thermodynamic parameters indicated spontaneous interaction between PGM and TGM (ΔG < 0) via endothermic (entropic) interactions (ΔH > 0). Notably, hydrophobic forces played a significant role in the network stabilisation of PGM−TGM complex (ΔS > 0). Rheometry analysis elucidates that the interaction maxima within TGM−PGM systems substantially elevate both shear viscosity (η), and the melting point (Tm), shifting from 6.75 ± 0.28 to 70.94 ± 2.21 (×10−3) Pa s (at 1 s−1), and 36.80 ± 0.80 to 48.20 ± 0.11 °C, respectively. Furthermore, the coexistence of these two macromolecular species results in a 3- to 4-fold dramatic increase in the viscoelastic moduli of the binary complex. These findings build a strong physicochemical basis for the interaction between TGM and PGM, with profound effects on the rhological behaviour of the latter; it also highlights the need to examine the biochemical/enzymatic aspects of said interactions, and their potential effects on mucosa and human physiology.

Thermodynamic origin of the affinity, selectivity, and domain specificity of metallothionein for essential and toxic metal ions.

The small Cys-rich protein metallothionein (MT) binds several metal ions in clusters within two domains. While the affinity of MT for both toxic and essential metals has been well studied, the thermodynamics of this binding has not. We have used isothermal titration calorimetry measurements to quantify the change in enthalpy (ΔH) and change in entropy (ΔS) when metal ions bind to the two ubiquitous isoforms of MT. The seven Zn2+ that bind sequentially at pH 7.4 do so in two populations with different coordination thermodynamics, an initial four that bind randomly with individual tetra-thiolate coordination and a subsequent three that bind with bridging thiolate coordination to assemble the metal clusters. The high affinity of MT for both populations is due to a very favourable binding entropy that far outweighs an unfavourable binding enthalpy. This originates from a net enthalpic penalty for Zn2+ displacement of protons from the Cys thiols and a favourable entropic contribution from the displaced protons. The thermodynamics of other metal ions binding to MT were determined by their displacement of Zn2+ from Zn7MT and subtraction of the Zn2+-binding thermodynamics. Toxic Cd2+, Pb2+, and Ag+, and essential Cu+, also bind to MT with a very favourable binding entropy but a net binding enthalpy that becomes increasingly favourable as the metal ion becomes a softer Lewis acid. These thermodynamics are the origin of the high affinity, selectivity, and domain specificity of MT for these metal ions and the molecular basis for their in vivo binding competition.

The Joint Solvation Interaction.

The solvent-induced interactions (SIIs) between flexible solutes can be separated into two distinct components: the solvation-induced conformational effect and the joint solvation interaction (JSI). The JSI quantifies the thermodynamic effect of the solvent simultaneously accommodating the solutes, generalizing the typical notion of the hydrophobic interaction. We present a formal definition of the JSI within the framework of the mixture expansion, demonstrate that this definition is equivalent to the SII between rigid solutes, and propose a method, partially connected molecular dynamics, which allows one to compute the interaction with existing free energy algorithms. We also compare the JSI to the more natural generalization of the hydrophobic interaction, the indirect solvent-mediated interaction, and argue that JSI is a more useful quantity for studying solute binding thermodynamics. Direct calculation of the JSI may prove useful in developing our understanding of solvent effects in self-assembly, protein aggregation, and protein folding, for which the isolation of the JSI from the conformational component of the SII becomes important due to the intra-species flexibility.

Optimizing Ligand-Receptor Binding Thermodynamics and Kinetics: The Role of Terahertz Wave Modulation in Molecular Recognition

Precision control over ligand-receptor recognition is critical in biochemistry and pharmacology. Traditional methods that alter reaction environments have limitations in fine-tuning the thermodynamic and kinetic aspects of biochemical reactions within biological systems. The advent of terahertz wave technology represents a significant breakthrough, providing a refined approach to modulating ligand-receptor interactions. This perspective explores the cutting-edge potential of terahertz waves in refining ligand-receptor recognition, featuring their innovative application in modulating neuronal functions. The capabilities of terahertz technology to selectively influence molecular interactions are discussed, highlighting its transformative potential for advancing therapeutic strategies and deepening our understanding of biological mechanisms.

The Role of Water Networks in Phosphodiesterase Inhibitor Dissociation and Kinetic Selectivity.

In search of new opportunities to develop Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) inhibitors that have selectivity over the off-target human PDE4 (hPDE4), different stages of a fragment-growing campaign were studied using a variety of biochemical, structural, thermodynamic, and kinetic binding assays. Remarkable differences in binding kinetics were identified and this kinetic selectivity was explored with computational methods, including molecular dynamics and interaction fingerprint analyses. These studies indicate that a key hydrogen bond between GlnQ.50 and the inhibitors is exposed to a water channel in TbrPDEB1, leading to fast unbinding. This water channel is not present in hPDE4, leading to inhibitors with a longer residence time. The computer-aided drug design protocols were applied to a recently disclosed TbrPDEB1 inhibitor with a different scaffold and our results confirm that shielding this key hydrogen bond through disruption of the water channel represents a viable design strategy to develop more selective inhibitors of TbrPDEB1. Our work shows how computational protocols can be used to understand the contribution of solvent dynamics to inhibitor binding, and our results can be applied in the design of selective inhibitors for homologous PDEs found in related parasites.

Enthalpic Classification of Water Molecules in Target-Ligand Binding.

Water molecules play various roles in target-ligand binding. For example, they can be replaced by the ligand and leave the surface of the binding pocket or stay conserved in the interface and form bridges with the target. While experimental techniques supply target-ligand complex structures at an increasing rate, they often have limitations in the measurement of a detailed water structure. Moreover, measurements of binding thermodynamics cannot distinguish between the different roles of individual water molecules. However, such a distinction and classification of the role of individual water molecules would be key to their application in drug design at atomic resolution. In this study, we investigate a quantitative approach for the description of the role of water molecules during ligand binding. Starting from complete hydration structures of the free and ligand-bound target molecules, binding enthalpy scores are calculated for each water molecule using quantum mechanical calculations. A statistical evaluation showed that the scores can distinguish between conserved and displaced classes of water molecules. The classification system was calibrated and tested on more than 1000 individual water positions. The practical tests of the enthalpic classification included important cases of antiviral drug research on HIV-1 protease inhibitors and the Influenza A ion channel. The methodology of classification is based on open source program packages, Gromacs, Mopac, and MobyWat, freely available to the scientific community.

Effects of ferritin iron loading, subunit composition, and the NCOA4-iron sulfur cluster on ferritin-NCOA4 interactions: An isothermal titration calorimetry study

Ferritin is a 24-mer protein nanocage that stores iron and regulates intracellular iron homeostasis. The nuclear receptor coactivator-4 (NCOA4) binds specifically to ferritin H subunits and facilitates the autophagic trafficking of ferritin to the lysosome for degradation and iron release. Using isothermal titration calorimetry (ITC), we studied the thermodynamics of the interactions between ferritin and the soluble fragment of NCOA4 (residues 383–522), focusing on the effects of the recently identified FeS cluster bound to NCOA4, ferritin subunit composition, and ferritin-iron loading. Our findings show that in the presence of the FeS cluster, the binding is driven by a more favorable enthalpy change and a decrease in entropy change, indicating a key role for the FeS cluster in the structural organization and stability of the complex. The ferritin iron core further enhances this association, increasing binding enthalpy and stabilizing the NCOA4-ferritin complex. The ferritin subunit composition primarily affects binding stoichiometry of the reaction based on the number of H subunits in the ferritin H/L oligomer. Our results demonstrate that both the FeS cluster and the ferritin iron core significantly affect the binding thermodynamics of the NCOA4-ferritin interactions, suggesting regulatory roles for the FeS cluster and ferritin iron content in ferritinophagy.

Structural determinants of Vibrio cholerae FeoB nucleotide promiscuity

Ferrous iron (Fe2+) is required for the growth and virulence of many pathogenic bacteria, including Vibrio cholerae (Vc), the causative agent of the disease cholera. For this bacterium, Feo is the primary system that transports Fe2+ into the cytosol. FeoB, the main component of this system, is regulated by a soluble cytosolic domain termed NFeoB. Recent reanalysis has shown that NFeoBs can be classified as either GTP-specific or NTP-promiscuous, but the structural and mechanistic bases for these differences were not known. To explore this intriguing property of FeoB, we solved the X-ray crystal structures of VcNFeoB in both the apo and the GDP-bound forms. Surprisingly, this promiscuous NTPase displayed a canonical NFeoB G-protein fold like GTP-specific NFeoBs. Using structural bioinformatics, we hypothesized that residues surrounding the nucleobase could be important for both nucleotide affinity and specificity. We then solved the X-ray crystal structures of N150T VcNFeoB in the apo and GDP-bound forms to reveal H-bonding differences surrounding the guanine nucleobase. Interestingly, isothermal titration calorimetry revealed similar binding thermodynamics of the WT and N150T proteins to guanine nucleotides, while the behavior in the presence of adenine nucleotides was dramatically different. AlphaFold models of VcNFeoB in the presence of ADP and ATP showed important conformational changes that contribute to nucleotide specificity among FeoBs. Combined, these results provide a structural framework for understanding FeoB nucleotide promiscuity, which could be an adaptive measure utilized by pathogens to ensure adequate levels of intracellular iron across multiple metabolic landscapes.

Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.

Binding thermodynamics and kinetics play critical roles in drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics of small molecules and flexible peptides using conventional molecular dynamics (cMD), due to limited simulation time scales. Based on our previously developed ligand Gaussian accelerated molecular dynamics (LiGaMD) method, we present a new approach, termed "LiGaMD3″, in which we introduce triple boosts into three individual energy terms that play important roles in small-molecule/peptide dissociation, rebinding, and system conformational changes to improve the sampling efficiency of small-molecule/peptide interactions with target proteins. To validate the performance of LiGaMD3, MDM2 bound by a small molecule (Nutlin 3) and two highly flexible peptides (PMI and P53) were chosen as the model systems. LiGaMD3 could efficiently capture repetitive small-molecule/peptide dissociation and binding events within 2 μs simulations. The predicted binding kinetic constant rates and free energies from LiGaMD3 were in agreement with the available experimental values and previous simulation results. Therefore, LiGaMD3 provides a more general and efficient approach to capture dissociation and binding of both small-molecule ligands and flexible peptides, allowing for accurate prediction of their binding thermodynamics and kinetics.