Current Topics in Medicinal Chemistry - Volume 18, Issue 27, 2018

Identifying drug binding sites and elucidating drug action mechanisms are important components in a drug discovery process. In this review, we briefly compared three different approaches (sequence- based methods, structure-based methods and probe-based molecular dynamics (MD) methods) to identifying drug binding sites, and concluded that probe-based MD methods are much more advantageous in dealing with flexible target macromolecules and digging out druggable macromolecule conformations for subsequent drug screening. The applications of MD simulation to studying drug-target interactions were demonstrated with different types of target molecules, including lipid membrane, protein and DNA. The results indicate that MD simulations with enhanced sampling methods provide a powerful tool to determine free energy profiles/surfaces and identify important intermediate states, which are essential for the elucidation of drug action mechanisms. The future development of methods in MD simulations will benefit and speed up the drug discovery processes.

Molecular Dynamics (MD) based computational co-solvent mapping methods involve the generation of an ensemble of MD-sampled target protein conformations and using selected small molecule fragments to identify and characterize binding sites on the surface of a target protein. This approach incorporates atomic-level solvation effects and protein mobility. It has shown great promise in the identification of conventional competitive and allosteric binding sites. It is also currently emerging as a useful tool in the early stages of drug discovery. This review summarizes efforts as well as discusses some methodological advances and challenges in binding site identification process through these co-solvent mapping methods.

Fragment based drug design (FBDD) is a structure guided ligand design approach used in the process of drug discovery. It involves identification of low molecular weight fragments as hits followed by determination of their binding mode using X-ray crystallography and/or NMR spectroscopy. X-ray protein crystallography is one of the most sensitive biophysical methods used for screening and is least prone to false positives. It also provides detailed structural information of the protein–fragment complex at the atomic level. The retrieved binding information facilitates the optimization of fragments into drug like molecules. These identified molecules bind efficiently with the target proteins and form high quality binding interactions. Fragment-based screening using X-ray crystallography is, therefore, an efficient method for identifying binding hotspots on proteins that can be further exploited by chemists and biologists for the discovery of new drugs. The recent advancements in FBDD technique are illustrated in this review along with recently published success stories of FBDD technique in drug discovery.

Background: People suffer from fatal diseases which are responsible for mortality. Potent devices and medicines are being developed to fight diseases caused by the microorganism for saving the lives of individuals. Highly pathogenic viruses and bacteria are being incorporated into biological warfare, which has become a major threat to mankind and causes the destruction of lives in a short span of time. Objective: The pathogen Bacillus anthracis, which is the causative of anthrax, is used in bioterrorism. Efforts are therefore being made to study the progress of biodefense drug discovery research in combating anthrax-based bioterrorism. Methods: This review describes the present status of the studies ontherapeutic measurement of anthrax toxin inhibitors towards inhibition of protective antigen, lethal and edema factors using chemometric and drug design tools to explore essential structural features for further design of active congeneric compounds. Results: The inhibitors estimated to show high activity through different models may be proposed for further synthesis and testing of biological activity in terms of anthrax toxin inhibition and cytotoxicity testing by in vitro and in vivo assays. Conclusion: Such an attempt is an insight of biodefense drug design against the dreadful threat to the nation due to anthrax-based terrorism and biological warfare.

A series of imidazothiazole and oxazolopyridine derivatives as human Silent Information Regulator 1 (SIRT1) activators were subjected to the integrated 2D and 3D QSAR approaches. The derived 3D QSAR models yielded high cross-validated q2 values of 0.682 and 0.628 for CoMFA and CoMSIA, respectively. The non-cross validated values of r2 training = 0.89; predictive r2 test = 0.69 for CoMFA and r2=0.87; predictive r2 test =0.67 for CoMSIA reflected the statistical significance of the developed model. The steric, electrostatic, hydrophobic and hydrogen bond acceptor interactions have been found important in describing the variation in human SIRT1 activation. Further, 2D QSAR model for the same dataset yielded high statistical significance and derived 2D model’s parameters corroborated with the 3D model in terms of features. Derived model was also validated by the crystal structure of active conformation of SIRT1. Developed models may be useful for the identification of potential novel human SIRT1 activators as a therapeutic agent.

Diabetes mellitus type 2 (DMT2) is a metabolic disease characterized by a chronic increase in glycemia that promotes several long-term complications and high mortality. Some enzymes involved in glycaemic control, such as α -(1,4)-glucosidase, have now been established as novel pharmacological targets. Coumarins have shown benefits in attenuating signs and complications of DMT2, including inhibition of this enzyme. In this work, new synthetic coumarins (bearing different amide and aryl substituents) were studied in vitro as inhibitors of α-(1,4)-glucosidase. Among them, five molecules proved to be excellent α-(1,4)-glucosidase inhibitors, being compound 7 (IC50 = 2.19 μM) about 200 times more potent than acarbose, a drug currently used for the treatment of DMT2. In addition, most of the coumarins presented uncompetitive inhibition for the α-(1,4)-glucosidase. Molecular docking studies revealed that coumarins bind to the active site of the enzyme in a more external area comparing to the substrate, without interfering with it, and displaying aromatic and hydrophobic interactions, as well as some hydrogen bonds. According to the results, aromatic interactions with two phenylalanine residues, 157 and 177, were the most common among the studied coumarins. This study is a step forward for the understanding of coumarins as potential anti-diabetic compounds displaying α-(1,4)-glucosidase inhibition.

Leishmaniasis is an infectious disease caused by protozoal parasites belonging to Leishmania genus. Different clinical outcomes can be observed depending on the parasite species and health condition of patients. It can range from single cutaneous lesion until deadly visceral form. The treatment of all forms of leishmaniasis is based on pentavalent antimonials, and in some cases, the second-line drug, amphotericin B is used. Beside the toxicity of both drugs, parasites can be resistant to antimonial in some areas of the world. This makes fundamental the characterization of new drugs with leishmanicidal effect. Thus, the aim of the present work was to study the leishmanicidal activity of drugs able to interfere with ergosterol pathway (fenticonazole, tioconazole, nystatin, rosuvastatin and voriconazole) against promastigote and amastigote forms of L.(L.) amazonensis, L.(V.) braziliensis and L.(L.) infantum, and its impact on morphological and physiological changes in L.(L.) amazonensis or in host macrophages. We observed that fenticonazole, tioconazole and nystatin drugs eliminated promastigote and intracellular amastigotes, being fenticonazole and nystatin the most selective towards amastigote forms. Rosuvastatin and voriconazole did not present activity against amastigote forms of Leishmania sp. In addition, the drugs with leishmanicidal activity interfered with parasite mitochondrion. Although drugs did not stimulate NO and H2O2, specially fenticonazole was able to alkalize infected host macrophages. These results suggest well established and non-toxic antifungal drugs can be repurposed and used in leishmaniasis.

Leishmaniasis is a poverty-related disease endemic in 98 countries worldwide, with morbidity and mortality increasing daily. All currently used first-line and second-line drugs for the treatment of leishmaniasis exhibit several drawbacks including toxicity, high costs and route of administration. Consequently, the development of new treatments for leishmaniasis is a priority in the field of neglected tropical diseases. The aim of this work is to develop computational models those allow the identification of new chemical compounds with potential anti-leishmanial activity. A data set of 116 organic chemicals, assayed against promastigotes of Leishmania amazonensis, is used to develop the theoretical models. The cutoff value to consider a compound as active one was IC50≤1.5μM. For this study, we employed Dragon software to calculate the molecular descriptors and WEKA to obtain machine learning (ML) models. All ML models showed accuracy values between 82% and 91%, for the training set. The models developed with k-nearest neighbors and classification trees showed sensitivity values of 97% and 100%, respectively; while the models developed with artificial neural networks and support vector machine showed specificity values of 94% and 92%, respectively. In order to validate our models, an external test-set was evaluated with good behavior for all models. A virtual screening was performed and 156 compounds were identified as potential anti-leishmanial by all the ML models. This investigation highlights the merits of ML-based techniques as an alternative to other more traditional methods to find new chemical compounds with anti-leishmanial activity.

Colorectal cancer possesses the third highest diagnostic rate and is the second leading cause of cancer death in the USA as reported by NIH. Epidermal Growth Factor Receptor (EGFR), a transmembrane protein, participates in PLC gamma-1, RAS-RAF-MEK-MAPKs, phosphatidylinositol-3 kinase, Akt pathways and plays a key role in normal functioning of cell division, cell differentiation, apoptosis and migration. This protein is found to be overexpressed in more than 60% of the colorectal cancers. Overexpressed EGFR advances the tumorigenic properties through cell cycle dysregulation and activates signaling pathways linked to cancer such as WNT/β-catenin, transforming growth factor β (TGF-β) and phosphoinositide-3-kinase (PI3K). Inhibiting the overexpressed EGFR protein has been proposed for the treatment and many inhibitors have been reported suppressing the activity of EGFR. However, patients in malignant state of cancer show resistance to those inhibitors, which open a wide space to research for the discovery of novel inhibitors. The present study employed Molecular Docking and Virtual Screening to find novel inhibitors with high affinity against EGFR. Molecular docking of existing inhibitors resulted in the compound titled as BGB-283 (PubChem CID-89670174) having the highest score, which was subjected to similarity search to retrieve the drugs with similar structure. The virtual screening concluded a compound SCHEMBL18435602 (PubChem CID-126517400) which revealed a better affinity with the target protein. A comparative study of both the compounds showed equivalent pharmacokinetic properties. These identified drugs have a high potential to act as EGFR inhibitors and can show promising results in the research of colorectal cancer.

Background: Inflammation and oxidative stress are very closely related to pathophysiological processes and linked to multiple chronic diseases. Traditionally, the coconut fruits were used in Guatemala for treatment of dermatitis and inflammation. Isolation of the anti-inflammatory agent from the hard shell of the coconut fruit was targeted in the current study. Methods: Fractionation of ethanolic extract of the coconut hard shell was done by using column chromatography, solvent treatments and TLC that led to the isolation of a molecule. Results and Discussion: Spectral characterization of the molecule by LC-MS/MS QTOF, FTIR, 1HNMR, 13C-NMR, HMQC and HMBC indicated that it is a novel keto fatty acid, which is named as nuciferoic acid. Hyaluronidase inhibitory potential of the nuciferoic acid was found to be moderate. It was further docked in all the ten cavities of hyaluronidase and was compared with the substrate hyaluronic acid. Cavity 1 and cavity 4 could be the probable sites of action on hyaluronidase for nuciferoic acid. ADME and toxicological characterization suggested that the key sites of metabolism on nuciferoic acid are C1, C2, C14 and C17. Toxicity prediction against 55 toxicological endpoints revealed that nuciferoic acid does not have any indication of existing toxicological features. Conclusion: A novel keto fatty acid, nuciferoic acid, from C. nucifera hard shell has been isolated and characterized. It was found to inhibit hyaluronidase activity, which indicated its potential application as an anti-inflammatory drug or as an adjuvant.