Response surface methodology in drug design: A case study on docking analysis of a potent antifungal fluconazole

Mulberrin inhibits Botrytis cinerea for strawberry storage by interfering with the bioactivity of 14α-demethylase (CYP51)

Currently, chemical agents hold great promise in preventing and combating Botrytis cinerea. However, the antifungal mechanism of some agents for B. cinerea remains rather vague, imposing restrictions on the research and development of novel antifungal inhibitors. In this work, we discovered that mulberrin (MBN), a natural compound from the root bark of Ramulus Mori, with an IC₅₀ of 1.38 μM together, demonstrated marked anti-14α-demethylase (CYP51) activity through high throughput virtual screening and in vitro bioactivity assay. The computational biology results demonstrated that MBN and its derivatives were bound to the catalytic activity region of CYP51, but only MBN could form a strong π-cation interaction with the Fe ion of heme in CYP51 via the 2-methylpent-2-ene moiety at atom C9. MBN had a stronger binding free energy than the other three compounds with CYP51, implying that the 2-methylpent-2-ene moiety at atom C9 is a critical pharmacophore for CYP51 inhibitors. Subsequently, through an antifungal test, MBN demonstrated excellent anti-B. cinerea activity by inhibiting CYP51 activity. The EC₅₀ values of MBN toward hyphal growth and spore germination in B. cinerea were 17.27 and 9.56 μg mL^-1, respectively. The bioactivity loss of CYP51 by direct interaction with MBN induced the increase of cell membrane permeability, membrane destruction, and cell death. Meanwhile, in the B. cinerea infection model, MBN significantly prolonged the preservation of strawberries by preventing B. cinerea from infecting strawberries and could be used as a potential natural preserving agent for storing fruits.

Synthesis, characterization, antimicrobial and antibiofilm activity, and molecular docking analysis of NHC precursors and their Ag-NHC complexes

Microorganisms attach to surfaces and interfaces and form biofilms which create a sheltered area for host cell response. Therefore, biofilms provide troubles in fields such as medicine, food, and pharmaceuticals. Inhibition of formation of biofilms through hindering of quorum sensing could be a method for the production of new generation antibiotics. In this study, four new benzimidazole type NHC precursors (1-allyl-3-benzyl-5,6-dimethylbenzimidazolium chloride, 1-allyl-3-(2,4,6-trimethylbenzyl)-5,6-dimethylbenzimidazolium chloride, 1-allyl-3-(2,3,5,6-tetramethylbenzyl)-5,6-dimethylbenzimidazolium chloride, and 1-allyl-3-(2,3,4,5,6-pentamethylbenzyl)-5,6-dimethylbenzimidazolium chloride and Ag-NHC complexes of these molecules were synthesized and characterized by elemental analysis, FT-IR spectroscopy, 1H, and 13C{1H} NMR spectroscopy, LC-MS, and single crystal crystallography. Antimicrobial and biofilm formation inhibition activities of the molecules were evaluated. In addition, the activities of the molecules were examined in detail by molecular docking analysis. According to the results obtained, higher activity was achieved with the complex molecules when compared with the benzimidazole derivative ligands.

Artocarpus altilis extracts as a food-borne pathogen and oxidation inhibitors: RSM, COSMO RS, and molecular docking approaches

Lipid oxidation and microbial contamination are the major factors contributing to food deterioration. Food additives like antioxidants and antibacterials can prevent food spoilage by delaying oxidation and preventing the growth of bacteria. Artocarpus altilis leaves exhibited biological properties that suggested its use as a new source of natural antioxidant and antimicrobial. Supercritical fluid extraction (SFE) was used to optimize the extraction of bioactive compounds from the leaves using response surface methodology (yield and antioxidant activity). The optimum SFE conditions were 50.5 °C temperature, 3784 psi pressure and 52 min extraction time. Verification test results (Tukey’s test) showed that no significant difference between the expected and experimental DPPH activity and yield value (99%) were found. Gas-chromatography –mass spectrometry (GC-MS) analysis revealed three major bioactive compounds existed in A. altilis extract. The extract demonstrated antioxidant and antibacterial properties with 2,3-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, ferric reducing ability of plasma (FRAP), hydroxyl radical scavenging activity, tyrosinase mushrrom inhibition of 41.5%, 8.15 ± 1.31 (µg of ascorbic acid equivalents), 32%, 37% and inhibition zone diameter of 0.766 ± 0.06 cm (B. cereus) and 1.27 ± 0.12 cm (E. coli). Conductor like screening model for real solvents (COSMO RS) was performed to explain the extraction mechanism of the major bioactive compounds during SFE. Molecular electrostatic potential (MEP) shows the probability site of nucleophilic and electrophilic attack during bacterial inhibition. Based on molecular docking study, non-covalent interactions are the main interaction occurring between the major bioactive compounds and bacteria (antibacterial inhibition).

Efficiency of Sophora flavescens-Fructus Ligustri Lucidi Drug Pairs in the Treatment of Liver Fibrosis Based on the Response Surface Method

The pairing of Sophora flavescens and Fructus Ligustri lucidi is taken from Shi Jinmo Medicine. The idea behind this pairing was inspired by the similarity in pharmacological effects of the two herbal drugs, both of which are known to be effective in the treatment and protection against liver fibrosis. To quantitatively study the extent of the interaction between these drugs and the effect of pairing on the treatment of liver fibrosis, an animal model of liver fibrosis mice was established by intraperitoneal injection of low-dose carbon tetrachloride. The drugs were then administered individually, or in predefined compatibility ratio pairs, by gavage, and the effects on indexes of liver fibrosis were observed. The multisynthetic index method was adopted using Matlab software in order to construct a three-dimensional response surface map of the integration effect and conduct interaction analysis of Sophora flavescens and Fructus Ligustri lucidi. The quadratic surface fitting pattern was designed by quadratic regression to determine the optimal range of each drug. The obtained results show that when the compatibility ratio of Sophora flavescens-Fructus Ligustri lucidi drug pairs is less than or equal to 1:1, their therapeutic effect is enhanced by synergy (interaction value ranging between -0.2 and -1). Overall, the synergy of the high-dose drug pairs is stronger than that of the low-dose drug pairs. The optimal dose ranges are 6~12 g and 8~17 g for Sophora flavescens and Fructus Ligustri lucidi, respectively.

Volatile component interaction effects on compatibility of Cyperi Rhizoma and Angelicae Sinensis Radix or Chuanxiong Rhizoma by UPLC-MS/MS and response surface analysis

Cyperi Rhizoma (Xiangfu) combined with either Angelicae Sinensis Radix (Danggui) or Chuanxiong Rhizoma (Chuanxiong) are herb pairs that are commonly used in clinical settings. To illustrate the herb-herb interactions that occur when extracts from these herbs are obtained together, ultra-high-performance liquid chromatography coupled with triple quadrupole electrospray tandem mass spectrometry and response surface analysis were used. Volatile components, α-cyperone, nootkatone, ligustilide, senkyunolide A and senkyunolide I, were accurately identified with high precision. When Xiangfu was combined with Danggui at a 1:1 ratio, or with Chuanxiong at a 1:1 or 2:1 ratio, the dissolution rates of α-cyperone and nootkatone from the herbs were greatly increased, compared to those obtained from Xiangfu extract alone. The dissolution rates of ligustilide, senkyunolide A and senkyunolide I from Danggui or Chuanxiong changed proportionally to changes in the ratios of Xiangfu with either Danggui or Chuanxiong. Response surface analysis results presented polynomial regression equations between the dissolution of tested compounds and the corresponding input variables, including compatibility proportions and solvent dosage. Based on the predicted results from response surface analysis, a combination of Xiangfu with Chuanxiong at a ratio of near 1:1, or with Danggui at 1:2, resulted in the maximum dissolution of five volatile components. Our established method could be applied to herb-herb interaction research, and the results may provide a scientific basis for the development of Cyperi Rhizoma-Chuanxiong Rhizoma, or Cyperi Rhizoma-Angelicae Sinensis Radix-based formulas and products.

An Efficient ABC_DE_Based Hybrid Algorithm for Protein-Ligand Docking

Protein–ligand docking is a process of searching for the optimal binding conformation between the receptor and the ligand. Automated docking plays an important role in drug design, and an efficient search algorithm is needed to tackle the docking problem. To tackle the protein–ligand docking problem more efficiently, An ABC_DE_based hybrid algorithm (ADHDOCK), integrating artificial bee colony (ABC) algorithm and differential evolution (DE) algorithm, is proposed in the article. ADHDOCK applies an adaptive population partition (APP) mechanism to reasonably allocate the computational resources of the population in each iteration process, which helps the novel method make better use of the advantages of ABC and DE. The experiment tested fifty protein–ligand docking problems to compare the performance of ADHDOCK, ABC, DE, Lamarckian genetic algorithm (LGA), running history information guided genetic algorithm (HIGA), and swarm optimization for highly flexible protein–ligand docking (SODOCK). The results clearly exhibit the capability of ADHDOCK toward finding the lowest energy and the smallest root-mean-square deviation (RMSD) on most of the protein–ligand docking problems with respect to the other five algorithms.

HIGA: A Running History Information Guided Genetic Algorithm for Protein-Ligand Docking

Protein-ligand docking is an essential part of computer-aided drug design, and it identifies the binding patterns of proteins and ligands by computer simulation. Though Lamarckian genetic algorithm (LGA) has demonstrated excellent performance in terms of protein-ligand docking problems, it can not memorize the history information that it has accessed, rendering it effort-consuming to discover some promising solutions. This article illustrates a novel optimization algorithm (HIGA), which is based on LGA for solving the protein-ligand docking problems with an aim to overcome the drawback mentioned above. A running history information guided model, which includes CE crossover, ED mutation, and BSP tree, is applied in the method. The novel algorithm is more efficient to find the lowest energy of protein-ligand docking. We evaluate the performance of HIGA in comparison with GA, LGA, EDGA, CEPGA, SODOCK, and ABC, the results of which indicate that HIGA outperforms other search algorithms.

Genetic algorithm with a crossover elitist preservation mechanism for protein-ligand docking

Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.

Plant bioactive molecules bearing glycosides as lead compounds for the treatment of fungal infection: A review

Despite therapeutic advancement in the treatment of fungal infections, morbidity and mortality caused by these infections are still very high. There are approximately 300 fungal species that are infectious and can cause a variety of diseases. At present, several synthetic antifungal drugs are in clinical practice, many of them, however, are vulnerable to multidrug-resistant strains of microbes, and thus compromising the overall treatment outcomes. Glycosides are naturally occurring plant secondary metabolites with important therapeutic potential and clinical utility. The aim of this review was to focus on the antifungal effects of glycosides in preclinical studies with possible mechanism(s) wherein described. Published research show significant susceptibility of different fungi towards phytoglycosides, mediated through multiple mechanisms. Further detailed studies are needed to explain the clinical applications and limitations of these glycosides.