GREEN: A program package for docking studies in rational drug design

Summary A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.     

表皮生长因子受体和抑制剂之间分子对接的研究

研究了表皮生长因子受体(EGFR)和4-苯胺喹唑啉类抑制剂之间的相互作用模式,表皮生长因子受体的三维结构通过同源蛋白模建的方法得到,而抑制剂和靶酶结合复合物结构则通过分子力学和分子动力学结合的方法计算得到。从模拟结果得到的抑制剂和靶酶之间的相互作用模式表明范德华相互作用、疏水相互作用以及氢键相互作用对抑制剂的活性都有重要的影响,抑制剂的苯胺部分位于活性口袋的底部,能够与受体残基的非极性侧链产生很强的范德华和疏水相互作用,抑制剂双环上的取代基团也能和活性口袋外部的部分残基形成一定的范德华和疏水性相互作用,而抑制剂喹唑啉环上的氮原子能和周围的残基形成较强的氢键相互作用,对抑制剂的活性有较大的影响,计算得到抑制剂和靶酶之间的非键相互作用能以及抑制剂和靶酶之间的相互作用信息能够很好地解释抑制剂活性和结构的关系,为全新抑制剂的设计提供了重要的结构信息。     

Furcatin 水解酶的三维结构模建和与furcatin 的对接研究

利用同源模建和动力学模拟方法，模建了furcatin水解酶（FH）的三维结构．并在这基础上，分析了活性位点的组成和结构．研究了furcatin与FH的对接．结果表明，Ser84，Arg146，Thr189，Thr234和Gly372在复合物的形成过程中起重要的作用．其中，Ser84，Argl46和Thr189是在FH的活性口袋的二糖部分的亚单位一1中重要的氨基酸，Thr234和Gly372是亚单位-2中重要的氨基酸．     

DREAM++: Flexible docking program for virtual combinatorial libraries

We present a set of programs, DREAM++ (Docking and Reaction programs using Efficient seArch Methods written in C++), for docking computationally generated ligands into macromolecular binding sites. DREAM++ is composed of three programs: ORIENT++, REACT++ and SEARCH++. The program ORIENT++ positions molecules in a binding site with the DOCK algorithm [1, 2]. Its output can be used as input to REACT++ and SEARCH++. The program REACT++ performs user-specified chemical reactions on a docked molecule, so that reaction products can be evaluated for three dimensional complementarity with the macromolecular site. The program SEARCH++ performs an efficient conformation search on the reaction products using a hybrid backtrack [3, 4] and incremental construction [5, 6] algorithm. We have applied the programs to HIV protease–inhibitor complexes as test systems. We found that we can differentiate high-affinity ligands based on several measures: interaction energies, occupancy of protein subsites and the number of successfully docked conformations for each product. Encouraged by the results in the test case, we applied the programs to propose novel inhibitors of HIV protease. These inhibitors can be generated by organic reactions using commercially available reagents. They are alternatives to the inhibitors synthesized by Glaxo [7, 8].     

Validation studies and proficiency testing

Genetically modified organisms (GMOs) entered the European food market in 1996. Current legislation demands the labeling of food products if they contain <1% GMO, as assessed for each ingredient of the product. To create confidence in the testing methods and to complement enforcement requirements, there is an urgent need for internationally validated methods, which could serve as reference methods. To date, several methods have been submitted to validation trials at an international level; approaches now exist that can be used in different circumstances and for different food matrixes. Moreover, the requirement for the formal validation of methods is clearly accepted; several national and international bodies are active in organizing studies. Further validation studies, especially on the quantitative polymerase chain reaction methods, need to be performed to cover the rising demand for new extraction methods and other background matrixes, as well as for novel GMO constructs.     

Validation of a computer program for atomic absorption analysis

 The approach to validation of a computer program for an analytical instrument as a component of the analytical method (using this instrument with the program) is discussed. This approach was used for validating a new program for atomic absorption analysis. The validation plan derived from this approach was based on minimising the influence of all steps of the analytical procedure on the analytical results obtained by the method. In this way significant changes in the results may be caused only by replacement of the previous program by the new one. The positive validation conclusion was based on the comparison of the results of the analysis of suitable reference materials obtained with the new program and with its precursor in the same conditions, and also on comparison of their deviations from the accepted reference values for these materials, with the corresponding uncertainties. Received: 25 January 1997 Accepted: 14 March 1997     

SKATE: A docking program that decouples systematic sampling from scoring

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in‐house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross‐docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin‐dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

SDOCK: a global protein-protein docking program using stepwise force-field potentials

Fast Fourier transform (FFT) method limits the forms of scoring functions in global protein-protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein-protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis-Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well-known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near-native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near-native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force-field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein-protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi-bin/down.cgi.     

Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies

Summary We have performed docking studies with the SYSDOC program on acetylcholinesterase (AChE) to predict the binding sites in AChE of huperzine A (HA), which is a potent and selective, reversible inhibitor of AChE. The unique aspects of our docking studies include the following: (i) Molecular flexibility of the guest and the host is taken into account, which permits both to change their conformations upon binding. (ii) The binding energy is evaluated by a sum of energies of steric, electrostatic and hydrogen bonding interactions. In the energy calculation no grid approximation is used, and all hydrogen atoms of the system are treated explicitly. (iii) The energy of cation- interactions between the guest and the host, which is important in the binding of AChE, is included in the calculated binding energy. (iv) Docking is performed in all regions of the host's binding cavity. Based on our docking studies and the pharmacological results reported for HA and its analogs, we predict that HA binds to the bottom of the binding cavity of AChE (the gorge) with its ammonium group interacting with Trp⁸⁴, Phe³³⁰, Glu¹⁹⁹ and Asp⁷² (catalytic site). At the the opening of the gorge with its ammonium group partially interacting with Trp²⁷⁹ (peripheral site). At the catalytic site, three partially overlapping subsites of HA were identified which might provide a dynamic view of binding of HA to the catalytic site.     

Development and validation of a modular, extensible docking program: DOCK 5

We report on the development and validation of a new version of DOCK. The algorithm has been rewritten in a modular format, which allows for easy implementation of new scoring functions, sampling methods and analysis tools. We validated the sampling algorithm with a test set of 114 protein-ligand complexes. Using an optimized parameter set, we are able to reproduce the crystal ligand pose to within 2 A of the crystal structure for 79% of the test cases using our rigid ligand docking algorithm with an average run time of 1 min per complex and for 72% of the test cases using our flexible ligand docking algorithm with an average run time of 5 min per complex. Finally, we perform an analysis of the docking failures in the test set and determine that the sampling algorithm is generally sufficient for the binding pose prediction problem for up to 7 rotatable bonds; i.e. 99% of the rigid ligand docking cases and 95% of the flexible ligand docking cases are sampled successfully. We point out that success rates could be improved through more advanced modeling of the receptor prior to docking and through improvement of the force field parameters, particularly for structures containing metal-based cofactors.     

Ligand-protein docking studies of potential HIV-1 drug compounds using the algorithm FlexX

Four compounds are docked to a pentameric bundle representing the transmembrane part of the Vpu protein from HIV-1. Employing the docking algorithm FlexX, their free energy of binding is estimated leading to the conclusion that potential drug candidates need to form H-bonds either with neighbouring or with n + 2 helices at the site of the serines within the bundle.     

Anti-cancer,anti-oxidant and molecular docking studies of thiosemicarbazone indole-based derivatives

Based on the structural elements of bioactive 3-substituted indoles, a new series of indole–thiosemicarbazone hybrid derivatives were designed, synthesized, and well-characterized using different spectral techniques. The intended scaffolds were screened for their in vitro anti-proliferative activities against breast cancer (MCF-7), lung cancer (A-549), and liver cancer (Hep-G2) cell lines, as well as their anti-oxidant properties. Cytotoxicity studies revealed that compound 6n was the most potent, at least threefold more potent than the commercially available reference drug etoposide, against A-549. In addition, morphological analysis by the acridine orange/ethidium bromide double staining test and flow cytometry analysis confirmed induction of apoptosis in the A-549 cells by compound 6n. In order to validate the experimental results, molecular studies were performed to achieve the possible binding interactions of the most potent compound (6n) and colchicine with tubulin as well as ANP with ATPase domain of topoisomerase IIα active sites. Moreover, the radical scavenging potential of the final derivatives was found to be excellent with the range of 0.015–0.630 µM, comparable to the standard ascorbic acid (0.655 µM).

     

Molecular docking studies of some new imidazole derivatives for antimicrobial properties

In modern drug designing, molecular docking is routinely used for understanding drug-receptor interaction. In the present study six imidazole derivatives containing substituted pyrazole moiety (2a,b and 4a–d) were synthesized. Structures of the newly synthesized compounds were characterized by spectral studies. Compounds were screened for their antibacterial activity. Compound 4c was found to be potent antimicrobial against Pseudomonas aeruginosa at concentrations of 1 and 0.5 mg/mL compared to standard drug Streptomycin. All the compounds were subjected to molecular docking studies for the inhibition of the enzyme l-glutamine: d-fructose-6-phosphate amidotransferase[GlcN-6-P] (EC 2.6.1.16). The in silico molecular docking study results showed that, all the synthesized compounds having minimum binding energy and have good affinity toward the active pocket, thus, they may be considered as good inhibitor of GlcN-6-P synthase.     

大肠杆菌中高丝氨酸琥珀酰基转移酶的同源模建与对接研究

利用同源模建和分子动力学模拟方法,模建了大肠杆菌中高丝氨酸琥珀酰基转移酶的三维结构.分析了活性位点的组成,从结构上佐证了Cys142而不是Lys47为亲核进攻的残基,并通过与其天然底物琥珀酰-辅酶A的对接研究,从理论上确认了对复合物形成起到重要作用的氨基酸残基.     

Synthesis,anticancer, molecular docking and QSAR studies of benzoylhydrazone

To find out effective anticancer compounds we synthesized (1–30) derivatives of 4-isopropylbenzoylhydrazone and evaluated for anticancer potential. The compounds 3, 9, 12, 23, 26 and 28 showed better activities ranging (0.39–1.1 µg/ml) than the standard (1.53 ± 0.01 µg/ml). In line with this, compounds 2, 6, 24, 25 and 29 exhibited better activities compared to the second standard (5FU 4.60 ± 0.01 µg/ml). The best molecular docked complex between the BRCA1 structure and the 1–30 derivatives were analyzed based on the Glide docked score and binding orientation for both the SP and XP mode. The 2D-QSAR analysis reflected a significant correlation between the experimental and the predicted biological activities. The above-mentioned compounds were also assessed by various spectroscopic techniques.     

Synthesis,antibacterial activity and docking studies of substituted quinolone thiosemicarbazones

Abstract

Fifteen 2-quinolone thiosemicarbazone derivatives of which eleven were new, were synthesized at room temperature. The key intermediate was the quinolone carbaldehyde, from which thiosemicarbazones were formed by the reaction of thiosemicarbazides with the aldehyde moiety. The structures of the synthesized compounds were elucidated by 1D and 2D-NMR spectroscopy and mass spectrometry. The synthesized compounds showed antibacterial activity with MBCs in the range 0.80 to 36.49?mM against Staphylococcus aureus, Staphylococcus aureus Rosenbach (MRSA), Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli and Salmonella typhimurium. The best activity was seen when a larger halogen such as chlorine and bromine were substituted at C-6 on the quinolone scaffold and when a planar phenyl group was present on the thiosemicarbazone moiety. Activity was reduced when a smaller fluorine atom was present at C-6 or when a methyl group was attached to the thiosemicarbazone. This group of compounds showed a high negative binding affinity, which suggested promising antimcrobial activity. The 6-chloro derivative with a phenyl group on the thiosemicarbazone had the greatest negative binding affinity.     

Probing the structures of leishmanial farnesyl pyrophosphate synthases: homology modeling and docking studies

Leishmania donovani and Leishmania major farnesyl pyrophosphate synthase ( LdFPPS and LmFPPS) are potential targets for the development of antileishmanial therapy. The protein sequence for LdFPPS was recently elucidated in our laboratory. Highly refined homology models were generated using the protein sequences of LdFPPS and the closely related LmFPPS enzyme. A ligand-refined model of LmFPPS with a bound bisphosphonate ligand was generated using restraint-guided molecular mechanics followed by quantum mechanics/molecular mechanics refinement. The ligand-refined model of LmFPPS was further validated through extensive pose validation, enrichment, and other docking studies involving known bisphosphonate inhibitors. The model was able to explain the critical binding site interactions and site-directed mutagenesis data obtained from experimental studies on related FPPS enzymes. The ligand-refined model in conjunction with the validated docking protocol could be utilized in the future for structure-based virtual screening and rational drug design studies against these targets.     

Screening and docking studies of natural phenolic inhibitors of carbonic anhydrase II

Carbonic anhydrase II (CA II) is an important enzyme complex with Zn²⁺, which is involved in many physiological and pathological processes, such as calcification, glaucoma and tumorigenicity. In order to search for novel inhibitors of CA II, inhibition assay of carbonic anhydrase II was performed, by which seven natural phenolic compounds, including four phenolics (grifolin, 4-O-methyl-grifolic acid, grifolic acid, and isovanillic acid) and three flavones (eriodictyol, quercetin and puerin A), showed inhibitory activities against CA II with IC₅₀s in the range of 6.37–71.73 μmol/L. Grifolic acid is the most active one with IC₅₀ of 6.37 _μmol/L. These seven phenolic compounds were proved to be novel natural carbonic anhydrase II inhibitors, which were obtained in flexible docking study with GOLD 3.0 software. Results indicated that the aliphatic chain and polar groups of hydroxyl and carboxyl are important to their inhibitory activities, providing a new insight into study on CA II potent inhibitors. Authors with the equal contribution Supported by the National Natural Science Foundation of China (Grant No. 30725048) and the Foundation of Chinese Academy of Sciences (West Light Program).