Letters in Drug Design & Discovery - Volume 16, Issue 4, 2019

Background: Pneumococcal conjugate vaccines (PCVs) in the past, have been constructed via chemical coupling of pneumococcal capsules to immunogenic carrier proteins. The PCVs implementation in developing countries was prevented by their high manufacturing costs. This issue can be overcome via the development of protein-based vaccines against pneumococci. Choline binding protein D (CBPD), fibronectin binding protein (FBP), and D-alanyl-D-alanine-carboxy peptidase (DDCP) were already identified as pneumococcal surface proteins able to elicit protection against S. pneumoniae serotype 19F. Methods: As antibody responses are necessary for protection against pneumococci, the aim of this study is, therefore, to design computationally a chimeric pneumococcal vaccine using B-cell epitope regions of CBPD, FBP, and DDCP. These regions were determined using results of Bepipred, BCPreds and CBTope programs. The most probable immunoprotective B-cell epitope region (MIBR) of each protein was identified using VaxiJen. MIBRs were highly conserved in common S. pneumoniae serotypes causing invasive pneumococcal disease worldwide. The conserved MIBRs were joined together using either flexible (Gly4Ser)2 linker or the rigid AspProArgValProSerSer linker to form antigens with molecular weights of 22.53 kDa and 22.74 kDa, respectively. Results and Discussion: The codon optimization was done for the chimeric antigens. Analysis of mRNAs secondary structures revealed no stable hairpins at 5' ends that could interfere with antigen expression. The 3D model of the antigen possessing the flexible linker contained alpha helix, whereas several beta sheets were observed in the tertiary structure of the antigen possessing the rigid linker and it did not have any alpha helixes. Moreover, the antigen-containing the rigid linker included a beta sheet in the C-terminus of DDCP MIBR, which showed 60% residue identity to the beta sheet in the same region of the partial structure of DDCP obtained from protein data bank. However, the other antigen did not contain any similar structural elements in DDCP MIBR. Conclusion: In silico analyses of physicochemical properties indicated that inclusion of the rigid linker instead of the flexible linker resulted in better stability of the chimeric antigen. In addition, using the rigid linker increased the probability of the protein soluble expression in Escherichia coli. Therefore, the chimeric antigen composed of conserved MIBRs joining via the rigid linker is predicted to be a suitable vaccine candidate, which could elicit protection against common pneumococcal serotypes.

Background: The present work describes antimicrobial, antimycobacterium and anti HIV-1 evaluation of newly synthesized 5-(4-Substituted-benzylidene)-3-[4-(5-methyl-benzothiazol- 2-yl)-phenyl]-2-phenyl-3,5-dihydro-imidazol-4-one (4a-o). The docking studies were performed in order to predict the potential binding affinities. Objective: The major aim of this study is to develop the new class of bezylidine candidate clubbed with benzothiazole with less toxicity and improved potency as antimicrobial, antitubercular and anti HIV-1. Methods: The titled compounds were characterized by spectral studies (IR, 1H NMR, 13C NMR and Mass). In vitro antimycobacterium activity was carried out using Lowenstein-Jensen medium method and antimicrobial activity using the broth microdilution method. The anti HIV-1 reverse transcriptase activity was determined by the colorimetric MTT method and inhibition of virusinduced cytopathogenicity in MT-4 cells. Results: Compound 4i (50 μM) showed better antifungal activity against A. clavatus. Compound 4g (50 μM) with 95% inhibition demonstrated good activity against M. tuberculosis H37Rv. Compound 4k showed CC50 (50 μM) against MT-4 (CD4+ Human T-cells containing an integrated HTLV-1 genome) cells by 50%, while 16 μM concentration value EC50 from the HIV-1 induced cytopathogenicity. Molecular docking study suggested that 4k interacted with the target with binding energy by Vina score (-10.3 Kcal/mol). Conclusion: The preliminary in vitro evaluation results revealed that some of the compounds have promising antimicrobial activities as well as antitubercular potency. Among the various substituents on benzylidene, the nitro group was the most beneficial for improving the anti-HIV-1 activity. Docking result suggested that 4k compound could be acting as a non-competitive or weak inhibitor of Reverse Transcriptase (RT).

Background: The main factor for the prolongation of the ulcer treatment in the gastrointestinal system would be Helicobacter pylori infection, which can possibly lead to gastrointestinal cancer. Triple therapy is the treatment of choice by today's standards. However, observed resistance among the bacterial strains can make the situation even worse. Therefore, there is a need to discover new targeted antibacterial therapy in order to make success in the eradication of H. pylori infections. Methods: The targeted therapy rule is to identify the related macromolecules that are responsible for the survival of the bacteria. Thus, 2-[(2',4'-difluoro-4-hydroxybiphenyl-3-yl)carbonyl]-N- (substituted)hydrazinocarbothioamide (3-13) and 5-(2',4'-difluoro-4-hydroxybiphenyl-3-yl)-4- (substituted)-2,4-dihydro-3H-1,2,4-triazole-3-thiones (14-17) were synthesized and evaluated for antibacterial activity in vitro against H. pylori. Results: All of the tested compounds showed remarkable antibacterial activity compared to the standard drugs (Ornidazole, Metronidazole, Nitrimidazin and Clarithromycin). Compounds 4 and 13 showed activity as 2μg/ml MIC value. Conclusion: In addition, we have investigated binding modes and energy of the compounds 4 and 13 on urease enzyme active by using the molecular docking tools.

Background: Indazoleacetic acids and their pharmaceutically acceptable salts have been claimed to be useful as anti-inflammatory, analgesic and antipyretic agents. They are active in the treatment of respiratory diseases such as asthma, bronchitis, allergies and obstructive pulmonary diseases. Objectives: We report herein a feasible study concerned about the design, synthesis, structure and in vitro antimicrobial activity of 3-arylindazole-1-acetic acids derivatives. Series of compounds were synthesized by alkylation of 3-arylindazoles. Method: Synthesized compounds were subjected to study the effect on microbial growth in vitro. All synthesized compounds were found to exhibit antibacterial activities against a range of grampositive (Bacillus subtilis, Staphylococcus aureus) and gram-negative bacteria (Shigella sonnei, Escherichia coli) by broth dilution method. Results: The synthesized compounds exhibited antibacterial activities comparable to fluoroquinolones and some compounds exhibited better activity. These findings suggest a great potential of 3-arylindazole-1-acetic acids as antibacterial compounds. Conclusion: 3-Arylindazole-1-acetic acids are potent antimicrobial agent better than their respective 3-arylindazoles that revealed moderate activity against both gram positive and gram negative bacteria.

Background: Nigella sativa L. (N. sativa) has been reported to have biological activities such as anti-bacterial, anti-inflammatory, anti-oxidant and anti-fungal activities. Objective: This study aims to develop N. Sativa colloidal-emulgel with the evaluation of its antibacterial, anti-oxidant and in-vivo irritation and sensation testing. Method: Colloidal-emulgel formulations were prepared for N. sativa using different surfactants (Sodium Lauryl Sulphate (S.L.S) and sucrose ester). N. sativa emulsion formulations were prepared using heat inversion technique. After that, the optimum formulation was mixed with Carbopol to produce the colloidal-emulgel. The droplet size, size distribution, and rheological behavior were measured for emulgel formulations. Anti-bacterial and anti-oxidant activities were also reported in the in vivo studies for sensitivity, irritancy and spreadability. Results: It was found that the sucrose ester was able to produce the optimum emulsion formulation with droplets size of less than 1 μm. In the anti-bacterial test for Staphylococcus aureus, it was found that emulgel has an inhibition zone of 2.5 cm in diameter, but the oil alone being 1.3 cm. According to MRSA, the inhibition zone for emulgel was 1.1 cm, but for oil, it was 0.5 cm in diameter. Emulgel does not show any irritation or sensitivity. Also it has a homogeneous appearance with a smooth texture. In addition, it shows fair mechanical properties, and easy spreadability with acceptable bio-adhesion. Conclusion: It is concluded that N. sativa emulgel has been prepared with dermatological and cosmeceutical benefits.

Background: Malaria Parasite relies heavily on signal transduction pathways to control growth, the progression of the life cycle and sustaining stress for its survival. Unlike kinases, Plasmodium's phosphatome is one of the smallest and least explored for identifying drug target for clinical intervention. PF14_0660 is a putative protein present on the chromosome 14 of Plasmodium falciparum genome. Methods: Multiple sequence alignment of PF14_0660 with other known protein phosphatase indicate the presence of phosphatase motif with specific residues essential for metal binding, catalysis and providing structural stability. PF14_0660 is a mixed α/β type of protein with several β -sheet and α-helix arranged to form βαβαβα sub-structure. The surface properties of PF14_0660 is conserved with another phosphate of this family, but it profoundly diverges from the host protein tyrosine phosphatase. PF14_0660 was cloned, over-expressed and protein is exhibiting phosphatase activity in a dose-dependent manner. Docking of Heterocyclic compounds from chemical libraries into the PF14_0660 active site found nice fitting of several candidate molecules. Results: Compound PPinh6, PPinh 7 and PPinh 5 are exhibiting antimalarial activity with an IC50 of 1.4 ± 0.2μM, 3.8 ± 0.3 μM and 9.4 ± 0.6μM respectively. Compound PPinh 6 and PPinh 7 are inhibiting intracellular PF14_0660 phosphatase activity and killing parasite through the generation of reactive oxygen species. Conclusion: Hence, a combination of molecular modelling, virtual screening and biochemical study allowed us to explore the potentials of PF14_0660 as a drug target to design anti-malarials.

Background: In this study, some aryl (5-chloro-benzofuran-2-yl) ketoximes and their ethers were synthesised to evaluate their antifungal activity against C. albicans, C. glabrata, C. krusei, and C. parapsilosis. Methods: The structure elucidation of the compounds was performed by IR, 1H-NMR, 13C-NMR and HR-MS spectroscopic data. ADME parameters of synthesised compounds 2a-2d, 3a-3d, 4a-4d were predicted by an in-silico study and it was determined that all synthesised compounds may have a good pharmacokinetic profile. Results: In the anticandidal activity studies, compounds 2c and 3c were found to be the most active compounds. The effect of compound 2c, on ergosterol biosynthesis of C. albicans, was determined by using the LC-MS-MS method. Conclusion: It was also docked in the active site of the lanosterol 14α-demethylase enzyme, and shown that there is a strong interaction between compound 2c and enzyme.

Background: Cancer is a major cause of mortality and morbidity and given the limitations of many current cancer drugs, there is great need to discover and develop novel treatments. An alternative to the conventional drug discovery path is to exploit new classes of natural compounds such as cyclotides. This peptide family is characterized by linked C- and N-termini and a structural fold called the cyclic cystine knot (CCK). The CCK fold is responsible for the exceptional enzymatic, chemical and thermal stability of cyclotides. Methods: In the present study, an alternative to traditional cancer treatments, involving new nanomaterials and nanocarriers allowing efficient cyclotide delivery, is proposed. Using the polymers Eudragit® L 100-55 and RS 30 D, the cyclotides kalata B2 and parigidin-br1 (PBR1) were nanocapsulated, and nanoparticles 91 nm and 188 nm in diameter, respectively, were produced. Results: An encapsulation rate of up to 95% was observed. In vitro bioassays showed that the nanostructured cyclotides were partially able to control the development of the colorectal adenocarcinoma cell line CACO2 and the breast cancer cell line MCF-7. Conclusion: Data reported herein indicate that nanoformulated cyclotides exhibit antitumor activity and sustained drug release. Thus, the system using Eudragit® nanocapsules seems to be efficient for cyclotide encapsulation and probably could be used to target specific tumors in future studies.

Background: Thiosemicarbazones and its derivatives received a great pharmaceutical importance due to their prominent biological activities. Methods: A series of disubstituted thiosemicarbazone derivatives (1-12) were designed and synthesized as pure compounds in good yield. All the synthesized compounds were analyzed by spectral data. The anticancer activity of all the compounds was performed against breast cancer MCF-7 and MDA-MB-231 cell lines. Results: Most of the compounds showed activity against breast cancer MCF-7 and MDA-MB-231 cell lines with (IC50 = 12.25 μM 128;’ 185.35 μM) and (IC50 = 12.97 μM 128;’ 107.33 μM), respectively. Compound 9 presented (IC50 = 12.76 μM and 12.97 μM) against MCF-7 and MDA-MB-231 cell lines, respectively. Conclusion: Compound 9, was found to exhibit significant anti-breast cancer activity. This compound was further evaluated for side population percent inhibition assay on the breast cancer cell line MCF-7 at 5 and 10 μM concentration. It showed superiority to block side population by more than 80% at 5 μM concentration compared to the reference drug verapamil.

Background: Hepatitis C Virus (HCV) infection is the major cause of hepatitis after transfusion. And HCV Nonstructural Protein 5A (NS5A) inhibitors have become a new hotspot in the study of HCV inhibitors due to their strong antiviral activity, rapid speed of viral removing and broad antiviral spectrum. Methods: Forty-five NS5A inhibitors were chosen to process three-dimensional quantitative structure- activity relationship (3D-QSAR) by using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models. A training set consisting of 30 compounds was applied to establish the models and a test set consisting of 15 compounds was applied to do the external validation. Results: The CoMFA model predicted a q2 value of 0.607 and an r2 value of 0.934. And the CoMSIA model predicted a q2 value of 0.516 and an r2 value of 0.960 established on the effects of steric, electrostatic, hydrophobic and hydrogen-bond acceptor. 0.713 and 0.939 were the predictive correlation co-efficients (r2pred) of CoMFA and CoMSIA models, respectively. Conclusion: These conclusions provide a theoretical basis for drug design and screening of HCV NS5A complex inhibitors.

Background: Superficial fungal infections are the most common fungal diseases in humans, affecting more than 25% of the population worldwide. Methods: In the present study, we have investigated the activity of kakuol, a natural compound isolated from the rhizomes of Asarum sieboldii, and some analogues, against various dermatophytes and pharmacologically relevant yeasts. Results: One of the tested compounds, 2-acryloyl-4,5-methylenedioxyphenol, showed a broadspectrum activity against most of the fungal species assayed, resulting particularly effective against dermatophyte strains (MIC values in the range of 0.25-0.5 μg/mL, two/four-fold lower than the positive control miconazole). Conclusion: The results suggest that this molecule can be considered a promising starting point for the development of new antifungal compounds.

Background: Catecholamines combined with boric/boronic acids are attractive chemical agents in drug design because some of their adducts have shown interesting biological activity. Scant information exists about their stability. Objective: The aim of the present theoretical study was to explore the role of boron in molecules that combine catecholamines and boric/boronic acids, with a particular interest in examining stability. Method: The methodology was based on the US GAMESS program using DFT with the B3LYP exchange-correlation functional and the 6-31G (d,p) split-valence basis set. Results: According to the current findings, the boron-containing compounds (BCCs) exhibit weaker bonding to the hydroxyls on the ethylamine moiety than to those in the aromatic ring. The strongest binding site of a hydroxyl group was often found to be in meta-position (relative to ethylamine moiety) for boron-free compounds and in para-position for BCCs. Nonetheless, the methyl substituent in the amino group was able to induce changes in this pattern. We analyzed feasible boronsubstituted structures and assessed the relative strength of the respective C-B bonds, which allowed for the identification of the favorable points for reaction and stability. Conclusion: It is feasible to form adducts by bonding on the amine and catechol sides of catecholamines. The presence of boron stabilizes the adducts in para-position. Since some of these BCCs are promising therapeutic agents, understanding the mechanisms of reaction is relevant for drug design.