Computational Docking Results Research Articles

Synthesis, Structural Investigations, and In Vitro/In Silico Bioactivities of Flavonoid Substituted Biguanide: A Novel Schiff Base and Its Diorganotin (IV) Complexes.

Quercetin is one of the most powerful bioactive dietary flavonoids. The in vivo biological study of quercetin is extremely difficult due to its very low solubility. However, diorganotin complexes of quercetin are more useful when contrasted with quercetin due to increased solubility. In the present study, quercetin, substituted biguanide synthesized in the form of Schiff base and its di-alkyl/aryl tin (IV) complexes were obtained by condensing Schiff base with respective di-alkyl/aryl tin (IV) dichloride. Advanced analytical techniques were used for structural elucidation. The results of biological screening against Gram-positive/Gram-negative bacteria and fungi showed that these diorganotin (IV) derivatives act as potent antimicrobial agents. The in silico investigation with dihydropteroate (DHPS) disclosed a large ligand-receptor interaction and revealed a strong relationship between the natural exercises and computational molecular docking results.

Novel alpha6 preferring GABA-A receptor ligands based on loreclezole

The family of GABA-A receptors contains nineteen mammalian subunits from which pentameric, GABA gated anion channels are assembled. The subunit encoded by the GABRA6 gene is highly expressed in the cerebellum and the receptors to which it contributes have recently been demonstrated to be a promising candidate as a novel drug target. Here we examined a series of loreclezole derivatives for potentially selective action at α6β3γ2 receptors with the help of computational methods and functional testing with the two-electrode voltage clamp technique. The synthetic routes to some previously published ligands were improved, and a new derivative was synthesized based on computational docking results. This new loreclezole derivative, [3-(2-chloro-4-methylphenyl)-3-methylbutanenitrile (40)], was shown to display stronger modulatory action in concatenated α6β3γ2 receptors compared to their α1β3γ2 counterpart. The hypothetical bound state structure provides valuable guidance for future design of selective therapeutics.

The study on biological activity and molecular docking of secondary metabolites from Bacillus sp. isolated from the mangrove plant Rhizophora apiculata Blume

Five known secondary metabolites, namely 2-(2-heptenyl)-3-methyl-4-quinolinone (1), 3-methyl-2-(2-nonenyl)-4-quinolinone (2), 2-phenylacetic acid (3), 4-hydroxybenzoic acid (4), and (-)-jasmonic acid (5) were isolated and identified from the crude extract of an endophytic bacterium Bacillus sp. RAR_M1_45 from the mangrove plant Rhizophora apiculata Blume. Cytotoxic assays showed that compounds 1 and 2 exhibited cytotoxicity against the tested cancer cell lines A549 (human lung carcinoma), MCF7 (human breast carcinoma) and KB (human mouth epidermal carcinoma) with IC50 values from 65.09 ± 2.06 to 97.88 ±4.16μg/mL, whereas antimicrobial assays showed that compounds 1–3 exhibited selective antimicrobial activity against plant pathogens with MICs of 16–64 μg/mL. Additionally, compounds 1–5 exhibited α-amylase and α-glucosidase inhibitory effects with IC50 values from 63.87 ± 4.23 to 649.9 ±17.5μg/mL and from 163.3 ± 10.66 to 960.4 ±8.62μg/mL, respectively. Experimental bioassays also revealed that the α-amylase and α-glucosidase inhibitory activities of the isolated compounds were consistent with computational docking results. Regarding ligand-7TAA systems, the potential stability of the complexes by molecular docking simulation was high consistence on the order of α-amylase inhibitory assays: 5 (DS -11.9 kcal.mol−1) >4 (DS -11.3 kcal.mol−1) >3 (DS -10.7 kcal.mol−1) >2 (DS -9.9 kcal.mol−1) >1 (DS -9.0 kcal.mol−1). Regarding ligand-3W37 systems, the potential stability of the complexes by molecular docking simulation was high consistence on the order of α-glucosidase inhibitory assays: 5 (DS -12.8 kcal.mol−1) >4 (DS -12.1 kcal.mol−1) >3 (DS -11.7 kcal.mol−1) >2 (DS -10.0 kcal.mol−1) >1 (DS -9.8 kcal.mol−1).

Acetyl-11-Keto-Beta Boswellic Acid (AKBA) Protects Lens Epithelial Cells Against H2O2-Induced Oxidative Injury and Attenuates Cataract Progression by Activating Keap1/Nrf2/HO-1 Signaling.

Age-related cataract (ARC) is one of the leading blinding eye diseases worldwide. Chronic oxidative stress and the apoptosis of human lens epithelial cells (HLECs) have been suggested to be the mechanism underlying cataract formation. Acetyl-11-keto-β-boswellic acid (AKBA) is a pentacyclic triterpene with antioxidative and antiapoptotic effects. In this study, we investigated the potential effects of AKBA on oxidative-induced HLECs injury and cataract formation. H2O2 was used to simulate HLECs oxidative injury in vitro, and Na2SeO3 was applied to establish an in vivo cataract model. In our current study, a cell counting kit-8 (CCK-8) assay was performed to evaluate the effects of H2O2 and AKBA on cell viability in vitro. Intracellular reactive oxygen species (ROS) levels were measured with the ROS assay to verify the antioxidant capacity of AKBA. Apoptotic cells were detected and measured by TUNEL staining and flow cytometry, and quantitative real-time (qRT)-PCR and Western blotting were applied to examine the transcription and expression of apoptosis-related proteins. Furthermore, immunofluorescence staining was performed to locate factor-erythroid 2-related factor 2 (Nrf2), and the protein levels of Nrf2, kelch-like ECH-associated protein 1 (Keap1) and heme oxygenase-1 (HO-1) were determined by Western blotting. Finally, we observed the degree of lens opacity and performed hematoxylin-eosin (H&E) staining to assess the protective effect of AKBA on cataract formation in vivo. AKBA increased HLECs viability under H2O2 stimulation, decreased intracellular ROS levels and alleviated the cell apoptosis rate in vitro. AKBA significantly decreased the expression of caspase-3 and Bax and increased the content of Bcl-2. The results of immunofluorescence and immunohistochemical staining proved that the expression and nuclear translocation of Nrf2 were activated with AKBA treatment in vivo and in vitro. Moreover, computational docking results showed that AKBA could bind specifically to the predicted Keap1/Nrf2 binding sites. After AKBA activation, Nrf2 dissociates from the Nrf2/Keap1 complex, translocates into the nucleus, and subsequently promotes HO-1 expression. In addition, AKBA attenuated lens opacity in selenite-induced cataracts. Overall, these findings indicated that AKBA alleviated oxidative injury and cataract formation by activating the Keap1/Nrf2/HO-1 cascade. Therefore, our current study highlights that AKBA may serve as a promising treatment for ARC progression.

Alchemilla viridiflora Rothm.: the potent natural inhibitor of angiotensin I-converting enzyme.

Alchemilla viridiflora Rothm., Rosaceae is a herbaceous plant widespread in central Greece, Bulgaria, North Macedonia and Serbia with Kosovo. Liquid chromatography-mass spectrometry analysis leads to the identification of 20 compounds in methanol extract, mainly ellagitannins and flavonoid glycosides. Given that various plant extracts have traditionally been used to treat hypertension and that some of the analyzed methanol extract constituents have beneficial cardiovascular effects, we hypothesized that some of these effects are achieved by inhibiting angiotensin I-converting enzyme (ACE). The dose-dependent ACE inhibitory activities of A. viridiflora and miquelianin were observed with an IC50 of 2.51 ± 0.00µg/mL of A. viridiflora extract compared to the IC50 of 5.4139 ± 0.00µM for miquelianin. The contribution of the single compounds to the tested activity was further analyzed through the in silico experimental approach. Computational docking results showed that tiliroside, ellagic acid pentose and galloyl-hexahydroxydiphenoyl-glucose exhibited even better binding affinity for the ACE active site than miquelianin, for which ACE activity was confirmed by an in vitro assay.

A novel non‑selective atypical PKC agonist could protect neuronal cell line from Aβ‑oligomer induced toxicity by suppressing Aβ generation.

Atypical protein kinase C (aPKCs) serve key functions in embryonic development by regulating apical-basal polarity. Previous studies have shed light on their roles during adulthood, especially in the development of Alzheimer's disease (AD). Although the crystal structure of PKCι has been resolved, an agonist of aPKCs remains to be discovered. In the present study, by using the Discovery Studio program and LibDock methodology, a small molecule library (K66-X4436 KINA Set) of compounds were screened for potential binding to PKCι. Subsequently, the computational docking results were validated using affinity selection-mass spectrometry, before in vitro kinase activity was used to determine the function of the hit compounds. A cell-based model assay that can mimic the pathology of AD was then established and used to assess the function of these hit compounds. As a result, the aPKC agonist Z640 was identified, which could bind to PKCι in silico, in vitro and in this cell-based model. Z640 was further confirmed as a non-selective aPKC agonist that can activate the kinase activity of both PKCι and PKCζ. In the cell-based assay, Z640 was found to protect neuronal cell lines from amyloid-β (Aβ) oligomer-induced cell death by reducing reactive oxygen species production and restore mitochondrial function. In addition, Z640 could reduce Aβ40 generation in a dose-dependent manner and shift amyloid precursor protein processing towards the non-amyloid pathway. To conclude, the present study is the first, to the best of the authors' knowledge to identify an aPKC agonist by combining computer-assisted drug discovery and cell-based assays. The present study also revealed that aPKC agonists have therapeutic potential for the treatment of AD.

Drug repurposing for COVID-19 using computational screening: Is Fostamatinib/R406 a potential candidate?

With the gradual increase in the COVID-19 mortality rate, there is an urgent need for an effective drug/vaccine. Several drugs like Remdesivir, Azithromycin, Favirapir, Ritonavir, Darunavir, etc., are put under evaluation in more than 300 clinical trials to treat COVID-19. On the other hand, several vaccines like Pfizer-BioNTech, Moderna, Johnson & Johnson’s Janssen, Sputnik V, Covishield, Covaxin, etc., also evolved from the research study. While few of them already gets approved, others show encouraging results and are still under assessment. In parallel, there are also significant developments in new drug development. But, since the approval of new molecules takes substantial time, drug repurposing studies have also gained considerable momentum. The primary agent of the disease progression of COVID-19 is SARS-CoV2/nCoV, which is believed to have ~89% genetic resemblance with SARS-CoV, a coronavirus responsible for the massive outbreak in 2003. With this hypothesis, Human-SARS-CoV protein interactions are used to develop an in-silico Human-nCoV network by identifying potential COVID-19 human spreader proteins by applying the SIS model and fuzzy thresholding by a possible COVID-19 FDA drugs target-based validation. At first, the complete list of FDA drugs is identified for the level-1 and level-2 spreader proteins in this network, followed by applying a drug consensus scoring strategy. The same consensus strategy is involved in the second analysis but on a curated overlapping set of key genes/proteins identified from COVID-19 symptoms. Validation using subsequent docking study has also been performed on COVID-19 potential drugs with the available major COVID-19 crystal structures whose PDB IDs are: 6LU7, 6M2Q, 6W9C, 6M0J, 6M71 and 6VXX. Our computational study and docking results suggest that Fostamatinib (R406 as its active promoiety) may also be considered as one of the potential candidates for further clinical trials in pursuit to counter the spread of COVID-19.

Insights into the Inhibition Mechanism of Human Pancreatic α-Amylase, a Type 2 Diabetes Target, by Dehydrodieugenol B Isolated from Ocimum tenuiflorum.

Use of human pancreatic α-amylase (HPA) inhibitors is one of the effective antidiabetic strategies to lower postprandial hyperglycemia via reduction in the dietary starch hydrolysis rate. Many natural products from plants are being studied for their HPA inhibitory activity. The present study describes isolation of dehydrodieugenol B (DDEB) from Ocimum tenuiflorum leaves using sequential solvent extraction, structure determination by one-dimensional (1D) and two-dimensional (2D) NMR analyses, and characterization as an HPA inhibitor using kinetics, binding thermodynamics, and molecular docking. DDEB uncompetitively inhibited HPA with an IC50 value of 29.6 μM for starch and apparent Ki′ of 2.49 and Ki of 47.6 μM for starch and maltopentaose as substrates, respectively. The circular dichroism (CD) study indicated structural changes in HPA on inhibitor binding. Isothermal titration calorimetry (ITC) revealed thermodynamically favorable binding (ΔG of −7.79 kcal mol–1) with a dissociation constant (Kd) of 1.97 μM and calculated association constant (Ka) of 0.507 μM. Molecular docking showed stable HPA–inhibitor binding involving H-bonds and Pi-alkyl, alkyl–alkyl, and van der Waals (vDW) interactions. The computational docking results support the noncompetitive nature of DDEB binding. The present study could be helpful for exploration of the molecule as a potential antidiabetic drug candidate to control postprandial hyperglycemia.

Voltammetric and Docking Investigation of the Binding Interaction between (E)-1-[(2-Phenoxyphenylimino)methyl]naphthalen-2-ol and Calf Thymus DNA

In vitro interaction between (E)-1-[(2-phenoxyphenylimino)methyl]naphthalen-2-ol (2-PPMN) and calf thymus DNA (ct-DNA) at physiological pH was investigated by means of square-wave (SW) voltammetry and computational docking techniques. SW voltammetry study for 2-PPMN at pH 7.40 showed a cathodic peak at −1.520 V. By adding of ct-DNA, the cathodic current of 2-PPMN decreased due to intermolecular interaction. The effect of temperature on this interaction was also studied using voltammetric studies. The binding constants were determined from voltammetric data. According to van’t Hoff equation, ΔH and ΔS values were calculated as 124.68 kJ mol–1 and 526.16 J mol–1 K–1, respectively. Thermodynamic binding studies of 2-PPMN with ct-DNA suggested that hydrophobic forces played a main role and entropy favoured. The computational docking results revealed that 2-PPMN bound to the minor groove of ct-DNA and this interaction had a binding energy of −7.4 kcal mol–1.

Rapanone, a naturally occurring benzoquinone, inhibits mitochondrial respiration and induces HepG2 cell death

Rapanone is a natural occurring benzoquinone with several biological effects including unclear cytotoxic mechanisms. Here we addressed if mitochondria are involved in the cytotoxicity of rapanone towards cancer cells by employing hepatic carcinoma (HepG2) cells and isolated rat liver mitochondria. In the HepG2, rapanone (20–40 μM) induced a concentration-dependent mitochondrial membrane potential dissipation, ATP depletion, hydrogen peroxide generation and, phosphatidyl serine externalization; the latter being indicative of apoptosis induction. Rapanone toxicity towards primary rats hepatocytes (IC50 = 35.58 ± 1.50 μM) was lower than that found for HepG2 cells (IC50 = 27.89 ± 0.75 μM). Loading of isolated mitochondria with rapanone (5–20 μM) caused a concentration-dependent inhibition of phosphorylating and uncoupled respirations supported by complex I (glutamate and malate) or the complex II (succinate) substrates, being the latter eliminated by complex IV substrate (TMPD/ascorbate). Rapanone also dissipated mitochondrial membrane potential, depleted ATP content, released Ca2+ from Ca2+-loaded mitochondria, increased ROS generation, cytochrome c release and membrane fluidity. Further analysis demonstrated that rapanone prevented the cytochrome c reduction in the presence of decylbenzilquinol, identifying complex III as the site of its inhibitory action. Computational docking results of rapanone to cytochrome bc1 (Cyt bc1) complex from the human sources found spontaneous thermodynamic processes for the quinone-Qo and Qi binding interactions, supporting the experimental in vitro assays. Collectively, these observations suggest that rapanone impairs mitochondrial respiration by inhibiting electron transport chain at Complex III and promotes mitochondrial dysfunction. This property is potentially involved in rapanone toxicity on cancer cells.

Nematicidal effect against Bursaphelenchus xylophilus of harmine quaternary ammonium derivatives, inhibitory activity and molecular docking studies on acetylcholinesterase

In the present study, we have investigated nematicidal effects against Bursaphelenchus xylophilus and inhibition potential, molecular docking of 43 harmine derivatives on acetylcholinesterase in vitro and in vivo. Among them, harmine quaternary ammonium derivatives 10, 11, 12 and 13 displayed promising nematicidal effects with 48 h LC50 values of 1.63, 1.63, 1.75 and 1.44 μg/mL, respectively and remarkable inhibition effects on acetylcholinesterase (IC50 values are 0.92, 0.90, 0.82, 0.07 μg/mL in vitro and 17.16, 14.56, 13.63, 3.06 μg/mL in vivo, respectively). The structure–activity analysis indicated that the presence of the methyl group in 1–position, the electron–donating substituents in 2–and 9–positions, bromine in 6–position, and the electron–withdrawing substituents in 7–position of carboline ring, could enhance the nematicidal effect and inhibition of acetylcholinesterase. Moreover, a molecular model was provided for the binding between compound 13 and the active site of acetylcholinesterase based on the computational docking results and helps us to optimize these new leading compounds.

Structure-activity relationship investigation of coumarin-chalcone hybrids with diverse side-chains as acetylcholinesterase and butyrylcholinesterase inhibitors.

Chalcones containing tertiary amine side-chains have potent activity as acetylcholinesterase (AChE) inhibitors. However, the effects of the location of the tertiary amine groups as well as of other groups on AChE and butyrylcholinesterase (BChE) activity have not been reported. Here, we report the synthesis and testing of 36 new coumarin-chalcone hybrids (5d-7j, 9d-11f, 12k-13m) against AChE and BChE. The nature and position of the chalcone substituents had major effects on inhibitory activity as well as selectivity for AChE over BChE. Compounds with para-substituted chalcone fragments in which the substituents were choline-like had potent activity against AChE and poor activity against BChE, while ortho-substituted analogs exhibited an opposite effect. Replacement of the terminal amine groups by amide, alkyl or alkenyl groups abrogated activity. Compound 5e showed potent inhibitory activity [Formula: see text]) and good selectivity for AChE over BChE (ratio 27.4), and a kinetic study showed that 5e exhibited mixed-type inhibition against AChE. Computational docking results indicate that 5e binds to Trp 279, Tyr334 and Trp 84 in AChE, but only to Trp 82 in BChE. Overall, the results show that coumarin-chalcone hybrids with choline-like side-chains have promising activity and selectivity against AChE and be promising therapeutic leads for Alzheimer's disease.

Molecular interaction studies of some Co(III)-surfactants with the transport protein.

The present work describes the synthesis and the molecular interaction of two single-chain Co(III)-coordinated surfactant complexes with a plasma protein, human serum albumin by using various biophysical and in silico techniques. The experimental data reveals that like ordinary classical surfactants, our metallosurfactants also have the tendency to associate themselves and form micelles at critical micelle concentration. The thermodynamic parameters (ΔH°, ΔS°, and ΔG°) derived from the experiment demonstrates that the alkyl chain length and the head group of the Co(III)-surfactant complexes played a vital role in the binding process. Both the physico-chemical and computational docking results indicated that the Co(III)-surfactant complexes are stabilized by hydrogen bonding, hydrophobic and/or van der Waals forces. Thus, the data acquired herein for the interesting class of surfactant complexes will be of significance in metal-based drug discovery and developmental research.

Synthesis and molecular docking studies of chrysin derivatives as antibacterial agents

In order to search for drugs with excellent antibacterial activities, a series of novel chrysin derivatives were designed, synthesized, and evaluated as antibacterial agents. Results of the preliminary antibacterial tests against six human pathogenic bacteria in vitro showed that these compounds exhibited activities to some extent, and some displayed excellent activities than the natural parent chrysin, while some were even more potent than the positive drug Penicillin. Moreover, the molecular model for the binding between compound 8c and the active site of Escherichia coli β-ketoacyl-acyl carrier protein synthase III (Escherichia coli FabH) was provided on the basis of the computational docking results.

Synthesis, characterization, crystal structure and DNA, HSA-binding studies of four Schiff base complexes derived from salicylaldehyde and isopropylamine

Four new Schiff base complexes (NiL2, CoL2, CuL2 and ZnL2) (HL: ((E)-2-((isopropylamino) methyl) phenol) were synthesized and characterized by CHN elemental analysis, FT-IR and single crystal X-ray diffraction technique. The crystallographic data reveal that in all complexes the metal centers are four-coordinated by two phenolate oxygen and two imine nitrogen atoms of two moles of Schiff base ligand HL and geometry around the metal center in all of them is distorted tetrahedral. In addition, 1H and 13C NMR techniques were employed for characterization of diamagnetic ZnL2 complex. The binding affinity of complexes with DNA (fish sperm DNA, FS-DNA) and Human Serum Albumin (HSA) were investigated using fluorescence quenching, chemometrics, UV–Vis spectroscopy, viscosity measurements and molecular docking methods. The obtained results revealed that the DNA and HSA affinity for binding to complexes are in the following order: CuL2>ZnL2>CoL2>NiL2 and NiL2>ZnL2>CuL2>CoL2. The distance between complexes and HSA was obtained based on the Förster’s theory of non-radiative energy transfer. The computational molecular docking results showed that H-bond interactions, hydrophobic interactions, π-π stacking and π-cation interactions have dominant role in the stability of HSA-ML2 (M: Cu, Co, Ni and Zn). The computational docking and viscosity results suggest that all metal complexes interact with DNA presumably by the groove binding mechanism.

Design, Synthesis, in vitro Antiproliferative Activity, Binding Modeling of 1,2,4,-Triazoles as New Anti-Breast Cancer Agents.

This article demonstrates the synthesis of 1,2,4-triazole derivatives and their applications in medicine particularly as anti-breast cancer agents which is a major issue of the present. The synthesized compounds were characterized by elemental analysis, FT-IR and NMR. DFT was used to study the quantum chemical calculations of geometries and vibrational wave numbers of 3-hydroxynaphthyl and p-tolyl substituted 1,2,4-triazoles in the ground state. The scaled harmonic vibrational frequencies obtained from the DFT method were compared with those of the FT-IR spectra and found good agreement. The synthesized 1,2,4-triazole-naphthyl hybrids were screened for the anticancer activity against MCF-7 breast cancer lines. Among them compounds 3 and 7 showed broad spectrum anticancer activity with IC50 values 9.7 μM and 7.10 μM, respectively and their activity is comparable to that of the standard drugs. The molecular model for binding between the compounds (1-8) and the active site of BRCA2 was obtained on the basis of the computational docking results and the structure-activity relationship.

Triazole derivatives with improved in vitro antifungal activity over azole drugs.

A series of triazole antifungal agents with piperidine side chains was designed and synthesized. The results of antifungal tests against eight human pathogenic fungi in vitro showed that all the compounds exhibited moderate-to-excellent activities. Molecular docking between 8d and the active site of Candida albicans CYP51 was provided based on the computational docking results. The triazole interacts with the iron of the heme group. The difluorophenyl group is located in the S3 subsite and its fluorine atom (2-F) can form H-bonds with Gly307. The side chain is oriented into the S4 subsite and formed hydrophobic and van der Waals interactions with the amino residues. Moreover, the phenyl group in the side chain interacts with the phenol group of Phe380 through the formation of π–π face-to-edge interactions.

<i>De Novo</i> Design of Non-coordinating Indolones as Potential Inhibitors for Lanosterol 14-α-Demethylase (CYP51)

The development of antifungal drugs that inhibit lanosterol 14-α-demethylase (CYP51) via non-covalent ligand interactions is a strategy that is gaining importance. A series of novel tetraindol-4-one derivatives with 1- and 2-(2,4-substituted phenyl) side chains were designed and synthesized based on the structure of CYP51 and fluconazole. The antifungal activities of these derivatives against eight human pathogenic filamentous fungi and yeast strains were evaluated in vitro by measuring the minimal inhibitory concentrations. Nearly all tested compounds 8a-g displayed activity against Candida tropicalis, Candida guilliermondii and Candida parapsilosis with a minimum inhibitory concentration (MIC) value until 8 µg mL(-1), on the other hand compounds 7a-g showed activity against Aspergillus fumigatus with a MIC value of 31.25 µg mL(-1). A molecular modeling study of the binding interactions between compounds 6, 7d, 8g and the active site of MtCYP51 was conducted based on the computational docking results.

Small Molecule Binding, Docking, and Characterization of the Interaction between Pth1 and Peptidyl-tRNA

Bacterial Pth1 is essential for viability. Pth1 cleaves the ester bond between the peptide and nucleotide of peptidyl-tRNA generated from aborted translation, expression of mini-genes, and short ORFs. We have determined the shape of the Pth1:peptidyl-tRNA complex using small angle neutron scattering. Binding of piperonylpiperazine, a small molecule constituent of a combinatorial synthetic library common to most compounds with inhibitory activity, was mapped to Pth1 via NMR spectroscopy. We also report computational docking results, modeling piperonylpiperazine binding based on chemical shift perturbation mapping. Overall these studies promote Pth1 as a novel antibiotic target, contribute to understanding how Pth1 interacts with its substrate, advance the current model for cleavage, and demonstrate feasibility of small molecule inhibition.

NMR-assisted computational studies of peptidomimetic inhibitors bound in the hydrophobic pocket of HIV-1 glycoprotein 41

Due to the inherently flexible nature of a protein-protein interaction surface, it is difficult both to inhibit the association with a small molecule, and to predict how it might bind to the surface. In this study, we have examined small molecules that mediate the interaction between a WWI motif on the C-helix of HIV-1 glycoprotein-41 (gp41) and a deep hydrophobic pocket contained in the interior N-helical trimer. Association between these two components of gp41 leads to virus-cell and cell-cell fusion, which could be abrogated in the presence of an inhibitor that binds tightly in the pocket. We have studied a comprehensive combinatorial library of α-helical peptidomimetics, and found that compounds with strongly hydrophobic side chains had the highest affinity. Computational docking studies produced multiple possible binding modes due to the flexibility of both the binding site and the peptidomimetic compounds. We applied a transferred paramagnetic relaxation enhancement experiment to two selected members of the library, and showed that addition of a few experimental constraints enabled definitive identification of unique binding poses. Computational docking results were extremely sensitive to side chain conformations, and slight variations could preclude observation of the experimentally validated poses. Different receptor structures were required for docking simulations to sample the correct pose for the two compounds. The study demonstrated the sensitivity of predicted poses to receptor structure and indicated the importance of experimental verification when docking to a malleable protein-protein interaction surface.