The Binding of Alpinia galanga Oil and Its Nanoemulsion to Mammal GABAA Receptors Using Rat Cortical Membranes and an In Silico Modeling Platform.

The anesthetic effect of Alpinia galanga oil (AGO) has been reported. However, knowledge of its pathway in mammals is limited. In the present study, the binding of AGO and its key compounds, methyl eugenol, 1,8-cineole, and 4-allylphenyl acetate, to gamma-aminobutyric acid type A (GABAA) receptors in rat cortical membranes, was investigated using a [3H]muscimol binding assay and an in silico modeling platform. The results showed that only AGO and methyl eugenol displayed a positive modulation at the highest concentrations, whereas 1,8-cineole and 4-allylphenyl acetate were inactive. The result of AGO correlated well to the amount of methyl eugenol in AGO. Computational docking and dynamics simulations into the GABAA receptor complex model (PDB: 6X3T) showed the stable structure of the GABAA receptor-methyl eugenol complex with the lowest binding energy of -22.16 kcal/mol. This result shows that the anesthetic activity of AGO and methyl eugenol in mammals is associated with GABAA receptor modulation. An oil-in-water nanoemulsion containing 20% w/w AGO (NE-AGO) was formulated. NE-AGO showed a significant increase in specific [3H]muscimol binding, to 179% of the control, with an EC50 of 391 µg/mL. Intracellular studies show that normal human cells are highly tolerant to AGO and the nanoemulsion, indicating that NE-AGO may be useful for human anesthesia.

Lipid Profile, Antioxidant and Antihypertensive Activity, and Computational Molecular Docking of Diatom Fatty Acids as ACE Inhibitors.

Diatoms, as single cell eukaryotic microalgae, are rich sources of lipids, which have either beneficial or detrimental effects on the prevention and treatment of many diseases. Gas chromatography-mass spectrometry (GC-MS) identified diatom lipids with high levels of essential fatty acids (EFAs), especially polyunsaturated FAs (PUFAs) containing both omega-3 and omega-6. Nutritional values of FAs indicated possible applications in the pharmaceutical, nutraceutical, and functional food industries. Diatom FAs showed antioxidative potential on harmful radicals by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) scavenging, with high inhibition of the angiotensin-converting enzyme (ACE) that causes cardiovascular disease (CVD) and hypertension. A computational molecular docking simulation confirmed the inhibition mechanisms of FAs on ACE, with comparable levels of binding free energy to chemically synthesized ACE drugs. Findings suggested that diatom lipids showed potential for use as alternative ACE inhibitors or food supplement for CVD prevention.

Characteristic Structural Knowledge for Morphological Identification and Classification in Meso-Scale Simulations Using Principal Component Analysis.

Meso-scale simulations have been widely used to probe aggregation caused by structural formation in macromolecular systems. However, the limitations of the long-length scale, resulting from its simulation box, cause difficulties in terms of morphological identification and insufficient classification. In this study, structural knowledge derived from meso-scale simulations based on parameters from atomistic simulations were analyzed in dissipative particle dynamic (DPD) simulations of PS-b-PI diblock copolymers. The radial distribution function and its Fourier-space counterpart or structure factor were proposed using principal component analysis (PCA) as key characteristics for morphological identification and classification. Disorder, discrete clusters, hexagonally packed cylinders, connected clusters, defected lamellae, lamellae and connected cylinders were effectively grouped.

Potential Anti-Alzheimer Agents from Guanidinyl Tryptophan Derivatives with Activities of Membrane Adhesion and Conformational Transition Inhibitions.

Guanidinyl tryptophan derivatives TGN1, TGN2, TGN3, and TGN4 were synthesized, and these compounds were shown to possess in vitro inhibitory activity for amyloid aggregation in a previous study. Nevertheless, the influence of the TGN series of compounds on the binding and permeation behaviors of an Aß monomer to the cell membranes was not elucidated. In this study, we investigated the effect of compounds in the TGN series on the behavior of an Aß monomer regarding its toxicity toward the bilayer lipid membrane using molecular dynamics (MD) simulation. MD simulations suggest that TGN4 is a potential agent that can interfere with the movement of the Aß monomer into the membrane. The MM-GBSA result demonstrated that TGN4 exhibits the highest affinity to the Aß1-42 monomer but has the lowest affinity to the bilayer. Moreover, TGN4 also contributes to a decrease in the binding affinity between the Aß1-42 monomer and the POPC membrane. Regarding the results of the binding mode and conformational analyses, a high number of amino-acid residues were shown to provide the binding interactions between TGN4 and the Aß1-42 monomer. TGN4 also reduces the conformational transition of the Aß1-42 monomer by means of interacting with the monomer. The present study presents molecular-level insights into how the TGN series of compounds affect the membrane adsorption and the conformational transition of the Aß1-42 monomer, which could be valuable for the further development of new anti-Alzheimer agents.

Effects on Steroid 5-Alpha Reductase Gene Expression of Thai Rice Bran Extracts and Molecular Dynamics Study on SRD5A2.

Steroid 5-alpha reductases (SRD5As) are responsible for the conversion of testosterone to dihydrotestosterone, a potent androgen, which is the aetiologic factor of androgenetic alopecia. This study aimed to compare the SRD5A gene expression suppression activity exerted by Thai rice bran extracts and their components and investigate the interactional mechanism between bioactive compounds and SRD5A2 using molecular dynamics (MD) simulation. Bran of Oryza sativa cv. Tubtim Chumphae (TRB), Yamuechaebia Morchor (YRB), Riceberry (RRB), and Malinil Surin (MRB), all rice milling by-products, was solvent-extracted. The ethanolic extract of TRB had the highest sum of overall bioactive compounds (γ-oryzanol; α-, ß-, and γ-tocopherol; phenolics; and flavonoids). Among all extracts, TRB greatly downregulated the expression of SRD5A1, SRD5A2, and SRD5A3; there were no significant differences between TRB and finasteride regarding SRD5A suppression. The linear relationship and principal component analysis supported that the α-tocopherol content was correlated with the SRD5A suppression exerted by TRB. Furthermore, MD simulation demonstrated that α-tocopherol had the highest binding affinity towards SRD5A2 by interacting with residues Phe118 and Trp201. Our findings indicate that α-tocopherol effectively downregulates the expression of SRD5A genes and inhibits SRD5A2 activity, actions that are comparable to standard finasteride. TRB, a source of α-tocopherol, could be developed as an anti-hair loss product.

Novel Multifunctional Ascorbic Triazole Derivatives for Amyloidogenic Pathway Inhibition, Anti-Inflammation, and Neuroprotection.

Alzheimer's disease (AD) is a common neurodegenerative disorder. The number of patients with AD is projected to reach 152 million by 2050. Donepezil, rivastigmine, galantamine, and memantine are the only four drugs currently approved by the United States Food and Drug Administration for AD treatment. However, these drugs can only alleviate AD symptoms. Thus, this research focuses on the discovery of novel lead compounds that possess multitarget regulation of AD etiopathology relating to amyloid cascade. The ascorbic acid structure has been designated as a core functional domain due to several characteristics, including antioxidant activities, amyloid aggregation inhibition, and the ability to be transported to the brain and neurons. Multifunctional ascorbic derivatives were synthesized by copper (I)-catalyzed azide-alkyne cycloaddition reaction (click chemistry). The in vitro and cell-based assays showed that compounds 2c and 5c exhibited prominent multifunctional activities as beta-secretase 1 inhibitors, amyloid aggregation inhibitors, and antioxidant, neuroprotectant, and anti-inflammatory agents. Significant changes in activities promoting neuroprotection and anti-inflammation were observed at a considerably low concentration at a nanomolar level. Moreover, an in silico study showed that compounds 2c and 5c were capable of being permeated across the blood-brain barrier by sodium-dependent vitamin C transporter-2.

Molecular modeling for potential cathepsin L inhibitor identification as new anti-photoaging agents from tropical medicinal plants.

Ultraviolet exposure can cause photoaging toward the human skin which is begun by the inflammation on the exposure area, also resulting in activation of a degradative enzyme cathepsin L. This enzyme is one of the interesting novel therapeutic targets for antiaging agents. Three plants, named Kleinhovia hospita, Aleurites moluccana, and Centella asiatica, are well-known in the tropical region as anti-inflammatory herbs. The aims of this study were to predict the antiaging activity of the 31 compounds from these plants via inhibition of cathepsin L. All compounds were minimized their energies and then used in molecular docking. After that, molecular dynamics (MD) simulation was employed for the 5 candidate ligands and the positive control; schinol. Interaction analysis results of the pre-MD and post-MD simulation structures were obtained. Furthermore, a toxicity test was performed using ADMET Predictor 7.1. Based on the molecular docking and the MD simulation results, kleinhospitine A, ß-amyrin, and castiliferol exhibited lower binding free energy than schinol (-27.0925, -28.6813, -26.0037 kcal/mol) and also had interactions with the S´ region binding site. The toxicity test indicated that ß-amyrin is the most potential candidate since it exhibited the lowest binding energy and the high safety level.

Tentative Peptide‒Lipid Bilayer Models Elucidating Molecular Behaviors and Interactions Driving Passive Cellular Uptake of Collagen-Derived Small Peptides.

Collagen contains hydroxyproline (Hyp), which is a unique amino acid. Three collagen-derived small peptides (Gly-Pro-Hyp, Pro-Hyp, and Gly-Hyp) interacting across a lipid bilayer (POPC model membrane) for cellular uptakes of these collagen-derived small peptides were studied using accelerated molecular dynamics simulation. The ligands were investigated for their binding modes, hydrogen bonds in each coordinate frame, and mean square displacement (MSD) in the Z direction. The lipid bilayers were evaluated for mass and electron density profiles of the lipid molecules, surface area of the head groups, and root mean square deviation (RMSD). The simulation results show that hydrogen bonding between the small collagen peptides and plasma membrane plays a significant role in their internalization. The translocation of the small collagen peptides across the cell membranes was shown. Pro-Hyp laterally condensed the membrane, resulting in an increase in the bilayer thickness and rigidity. Perception regarding molecular behaviors of collagen-derived peptides within the cell membrane, including their interactions, provides the novel design of specific bioactive collagen peptides for their applications.

Depletion of ß-sitosterol and enrichment of quercetin and rutin in Cissus quadrangularis Linn fraction enhanced osteogenic but reduced osteoclastogenic marker expression.

BACKGROUND: Cissus quadrangularis Linn. (CQ) has been used in Indian and Thai traditional medicine for healing bone fractures because of numerous active ingredients in CQ. It is still unclear which compounds are the active ingredients for bone formation. METHODS: The molecular docking technique, the ethanolic extraction along with hexane fractionation, and an in vitro experiment with a human osteoblast cell line (MG-63) were used to narrow down the active compounds, to prepare the CQ extract, and to test biological activities, respectively. RESULTS: The molecular docking technique revealed that quercetin and ß-sitosterol had highest and lowest potential to bind to estrogen receptors, respectively. Compared to the crude ethanol extract (P1), the ethanolic fraction (P2) was enriched with rutin and quercetin at 65.36 ± 0.75 and 1.06 ± 0.12 mg/g, respectively. Alkaline phosphatase (ALP) activity was significantly enhanced in osteoblasts exposed to the P2 in both tested concentrations. The amount of hydroxyproline was slightly increased in the P1 treatment, while osteocalcin was inhibited. Moreover, the P2 significantly activated osteoprotegerin (OPG) and inhibited receptor activator of nuclear factor κ ligand (RANKL) expression. CONCLUSIONS: Taken together, the enriched rutin and quercetin fraction of CQ triggered the molecules involved in bone formation and the molecules inhibiting bone resorption.

Synthesis of polymeric hydrogels incorporating chlorhexidine gluconate as antibacterial wound dressings.

Antibacterial hydrogels based on poly(sodium 2-acrylamido-2-methylpropane sulfonate) and gelatin and incorporating chlorhexidine gluconate (CHG) as a drug were fabricated. The work focused on the effects of varying the CHG concentration. The hydrogel containing 0.02% w/v of CHG was chosen as the drug-loaded hydrogel for comparison with the hydrogel with no drug. From the drug release results, it was found that only 2-5% CHG was released, indicating that the CHG strongly interacted with the hydrogel network. To confirm the antibacterial efficiency of the hydrogels, the shake-flask method and scanning electron microscopy were employed. The antibacterial activity of the drug-loaded hydrogels showed a 7-log reduction for S. aureus gram-positive and a 5-6-log reduction for E. coli gram-negative bacteria. In addition, an MTT assay was performed to evaluate their potential cytotoxicity and showed a percentage cell viability after 24 h of more than 70% which classified them as being non-cytotoxic. In conclusion, the hydrogels containing CHG are considered as one of the interesting candidates for potential biomedical use as antibacterial wound dressings. Further in vivo investigations are planned.[Figure: see text].

Discovery of potential sclerostin inhibitors from plants with loop2 region of sclerostin inhibition by interacting with residues outside Pro-Asn-Ala-Ile-Gly motif.

Sclerostin, an antagonist of the Wnt/ß-catenin signaling pathway, was discovered as a potential therapeutic target for stimulating bone formation in osteoporosis. In this study, molecular docking was employed to predict the binding of 29 herbal compounds, which were reported as bone formation stimulators, to the loop2 region of sclerostin. Then, the 50 ns molecular dynamics (MD) simulation of the complexes between sclerostin and the top 10 hits obtained from molecular docking were carried out. Root mean square deviations (RMSDs) analysis of MD trajectories pointed out that all ligands-complexes remain stable throughout the duration of MD simulations. In addition, the molecular mechanics/generalized born surface area (MM/GBSA) binding free energy and energy decomposition analyses were determined. The results here suggested that baicalin is the most promising inhibitor of sclerostin. Interestingly, baicalin binds to sclerostin via the hydrophobic interaction with the amino acid residues on loop2 region but outside the Pro-Asn-Ala-Ile-Gly (PNAIG) motif, particularly the Arg-Gly-Lys-Trp-Trp-Arg (RGKWWR) motif. This finding could be a novel strategy for developing new sclerostin inhibitors in the future.Communicated by Ramaswamy H. Sarma.

Molecular modeling investigation of the potential mechanism for phytochemical-induced skin collagen biosynthesis by inhibition of the protein phosphatase 1 holoenzyme.

The most prominent feature of UV-induced photoaged skin is decreased type 1 procollagen. Increase of the TGF-ß/Smad signaling through inhibition of the TßRI dephosphorylation by the GADD34-PP1c phosphatase complex represents a promising strategy for the increase in type 1 collagen production and prevention of UV-induced skin photoaging. In this study, the molecular docking and dynamics simulations, and pharmacophore modeling method were run to investigate a possible binding site as well as binding modes between apigenin, daidzein, asiaticoside, obovatol, and astragaloside IV and PP1c. Through docking study, the possible binding site for these phytochemicals was predicted as the hydrophobic (PP1-substrate binding) groove. The result indicates that PP1 is the significant target of these compounds. Moreover, the 20,000-ps MD simulations present that the binding locations and modes predicted by the docking have been slightly changed considering that the MD simulations proffer more reliable details upon the protein-ligand recognition. The MM-GBSA binding free energy calculations and pharmacophore modeling rationally identify that the highly hydrophobic surfaces/pockets at close proximity of the catalytic core are the most favorable binding locations of the herbal compounds, and that some experimental facts upon a possible mechanism of increase in collagen biosynthesis can be explained. The present study theoretically offers the reliable binding target of the herbal compounds, and therefore helps to understanding the action mechanism for natural small molecules that enhance collagen production.

An integrated molecular modeling approach for the tryptase monomer-curcuminoid recognition analysis: conformational and bioenergetic features.

Human mast cell tryptase has been shown as an activating enzyme in matrix degradation process. The previous study suggest that tryptase either alone or in joining with activation of metalloproteinases, can associate in extra cellular matrix damage and the possible destruction of the basement membrane resulting in photoaging. Therefore the inhibition of tryptase activity is one of the most important therapeutic strategies against the photoaging. Curcumin has been shown to be a potential agent for preventing and/or treating the photoaging induced by UV radiation. However, the protective effect of curcumin against the photoaging through the tryptase inhibition is still inadequately understood. In this work, computational methods to characterize the structural framework and define the atomistic details of the determinants for the tryptase inhibition mechanism by curcuminoids were performed. By molecular docking, three putative binding models able to efficiently bind all curcuminoids were identified. Analysis of molecular dynamics simulations revealed that cyclocurcumin, curcumin glucuronide, and curcumin, the most effective inhibitors from the three models, modified significant tryptase monomer rigidity by binding in all the possible sites. The result of these binding events is the suppression of the functional enzymatic motions involving the binding of substrates to the catalytic site. On the basis of this finding may thus be beneficial for the development of new natural inhibitors for the therapeutic remedy of photoaging, targeting and modulating the activity of tryptase.

Molecular modeling of non-covalent binding of Ligustrum lucidum secoiridoid glucosides to AP-1/matrix metalloproteinase pathway components.

Ligustrum lucidum secoiridoid glucosides have been demonstrated to treat various types of diseases such as inflammation, pain, hepatotoxicity and hyperlipidermic as well as tonic for liver and kidney. Matrix metalloproteinases (MMPs) play a key role upon the pathology of photoaging. The present computational study showed that among the six secoiridoid glucosides (ligustroside, lucidumoside A, lucidumoside C, neonuezhenide, oleoside dimethylester, and oleuropein), ligustroside and lucidumoside A competitively inhibit all MMP-1, MMP-3, and MMP-9 activities in the docking models. The molecular docking analysis revealed a network of interactions between MMP-1, MMP-3, and MMP-9 and the ligands; ligustroside and lucidumoside A, and oxygen-containing and hydrophobic functional groups appear to be responsible for these enhanced interactions. The effect of ligustroside and lucidumoside A on the transcription factor AP-1 action was also investigated using molecular docking and dynamics simulations. The experiments suggested that inhibition of an AP-1-DNA complex formation could be on account of the direct interference of AP-1 binding onto the DNA binding sequence by ligustroside and lucidumoside A. The results suggest that both compounds have the highest potential for application as an anti-aging agent with the MMP inhibitory and anti-transcriptional activities.

A significant mechanism of molecular recognition between bioflavonoids and P-glycoprotein leading to herb-drug interactions.

Inhibition of P-glycoprotein (P-gp)'s function may conduct significant changes in the prescription drugs' pharmacokinetic profiles and escalate potential risks in taking place of drug/herb-drug interactions. Computational modeling was advanced to scrutinize some bioflavonoids which play roles in herb-drug interactions as P-gp inhibitors utilizing molecular docking and pharmacophore analyses. Twenty-five flavonoids were utilized as ligands for the modeling. The mouse P-gp (code: 4Q9H) was acquired from the PDB. The docking was operated utilizing AutoDock version 4.2.6 (Scripps Research Institute, La Jolla, CA) against the NBD2 of 4Q9H. The result illustrated the high correlation between the docking scores and observed activities of the flavonoids and the putative binding site of these flavonoids was proposed and compared with the site for ATP. To evaluate hotspot amino acid residues within the NBD2, Binding modes for the ligands were achieved using LigandScout to originate the NBD2-flavonoid pharmacophore models. The results asserted that these inhibitors competed with ATP for binding site in the NBD2 (as competitive inhibitors) including the hotspot residues which associated with electrostatic and van der Waals interactions with the flavonoids. In MD simulation of eight delegated complexes selected from the analyzed flavonoid subclasses, RMSD analysis of the trajectories indicated the residues were stable throughout the duration of simulations.

Molecular modeling elucidates the cellular mechanism of synaptotagmin-SNARE inhibition: a novel plausible route to anti-wrinkle activity of botox-like cosmetic active molecules.

Synaptotagmin 1 (Syt1) is the Ca2+ sensor protein with an essential role in neurotransmitter release. Since the wrinkle formation is due to the excessive muscle fiber stimulation in the face, a helpful stratagem to diminish the wrinkle line intenseness is to weaken the innervating neuron activity through Syt1 inhibition which is one of the possible therapeutic strategies against wrinkles. Recently, experimental evidence showed that botox-like peptides, which are typically used as SNARE modulators, may inhibit Syt1. In this work, we applied molecular modeling to (1) characterize the structural framework and (2) define the atomistic information of the factors for the inhibition mechanism. The modeling identified the plausible binding cleft able to efficiently bind all botox-like peptides. The MD simulations revealed that all peptides induced significant Syt1 rigidity by binding in the cleft of the C2A-C2B interface. The consequence of this binding event is the suppression of the protein motion associated with conformational change of Syt1 from the closed form to the open form. On this basis, this finding may therefore be of subservience for the advancement of novel botox-like molecules for the therapeutic treatment of wrinkle, targeting and modulating the function of Syt1.

Estimation of Retention Time in GC/MS of Volatile Metabolites in Fragrant Rice Using Principle Components of Molecular Descriptors.

A quantitative structure-retention relationship (QSRR) study was applied for an estimation of retention times of secondary volatile metabolites in Thai jasmine rice. In this study, chemical components in rice seed were extracted using solvent extraction, then separated and identified by gas chromatography-mass spectrometry (GC-MS). A set of molecular descriptors was generated for these substances obtained from GC-MS analysis to numerically represent the molecular structure of such compounds. Principal component analysis (PCA) and principal component regression analysis (PCR) were used to model the retention times of these compounds as a function of the theoretically derived descriptors. The best fitted regression model was obtained with R-squared of 0.900. The informative chemical properties related to retention time were elucidated. The results of this study demonstrate clearly that the combination of molecular weight and autocorrelation functions of two dimensional interatomic distance, which are molecular polarizability, atom identity, sigma charge, sigma electronegativity and polarizability, can be considered as comprehensive factors for predicting the retention times of volatile compounds in rice.

Insight into the molecular mechanism of P-glycoprotein mediated drug toxicity induced by bioflavonoids: an integrated computational approach.

In this work, molecular docking, pharmacophore modeling and molecular dynamics (MD) simulation were rendered for the mouse P-glycoprotein (P-gp) (code: 4Q9H) and bioflavonoids; amorphigenin, chrysin, epigallocatechin, formononetin and rotenone including a positive control; verapamil to identify protein-ligand interaction features including binding affinities, interaction characteristics, hot-spot amino acid residues and complex stabilities. These flavonoids occupied the same binding site with high binding affinities and shared the same key residues for their binding interactions and the binding region of the flavonoids was revealed that overlapped the ATP binding region with hydrophobic and hydrophilic interactions suggesting a competitive inhibition mechanism of the compounds. Root mean square deviations (RMSDs) analysis of MD trajectories of the protein-ligand complexes and NBD2 residues, and ligands pointed out these residues were stable throughout the duration of MD simulations. Thus, the applied preliminary structure-based molecular modeling approach of interactions between NBD2 and flavonoids may be gainful to realize the intimate inhibition mechanism of P-gp at NBD2 level and on the basis of the obtained data, it can be concluded that these bioflavonoids have the potential to cause herb-drug interactions or be used as lead molecules for the inhibition of P-gp (as anti-multidrug resistance agents) via the NBD2 blocking mechanism in future.

3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity.

The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R (2)=0.927, [Formula: see text], SEE=0.197, F=33.849 and q (2)=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion.

Pairwise decomposition of residue interaction energies of single chain Fv with HIV-1 p17 epitope variants.

Computational assisted modeling was carried out to investigate the importance of specific residues in the binding site of scFv. In this study, scFv against HIV-1 epitope at the C-terminal on p17 (scFv anti-p17) was used as a candidate molecule for evaluating the method. The wild-type p17 and its nine natural mutants were docked with scFv anti-p17. Potential mean force (PMF) scores predicted the most favorable binding interaction, and the correlation agreed well with the corresponding activity data from the peptide based ELISA. In the interaction with solvent molecules, the 3D structures of scFv anti-p17 and selected peptide epitopes were further investigated by molecular dynamics (MDs) simulation with the AMBER 9 program. Post-processing of the snapshot at equilibrium was performed to evaluate the binding free energy and pairwise decomposition or residue-based energy calculation of complexes in solution using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) protocol. Our results demonstrated that the specific residues located in the complementary determining regions (CDRs) of scFv anti-p17, MET100, LYS101, ASN169, HIS228, and LEU229, play a crucial role in the effective binding interaction with the absolute relative decomposed energy more than 2.00 kcal/mol in comparison to the original substrate.