Letters in Drug Design & Discovery - Volume 17, Issue 11, 2020

Background: Fibroblast growth factors (FGFs) and their high affinity receptors (FGFRs) play a major role in cell proliferation, differentiation, migration, and apoptosis. Aberrant FGFR signaling pathway might accelerate development in a broad panel of malignant solid tumors. However, the full application of most existing small molecule FGFR inhibitors has become a challenge due to the potential target mutation. Hence, it has attracted a great deal of attention from both academic and industrial fields for hunting for novel FGFR inhibitors with potent inhibitory activities and high selectivity. Objective: Novel 5-amino-1H-pyrazole-1-carbonyl derivatives were designed, synthesized, and evaluated as FGFR inhibitors. Methods: A series of 5-amino-1H-pyrazole-1-carbonyl derivatives were established by a condensation of the suitable formyl acetonitrile derivatives with either hydrazine or hydrazide derivatives in the presence of anhydrous ethanol or toluene. The inhibitory activities of the target compounds were screened against the FGFRs and two representative cancer cell lines. Tests were carried out to observe the inhibition of 8e against FGFR phosphorylation and downstream signal phosphorylation in human gastric cancer cell lines (SNU-16). The molecular docking of all the compounds were performed using Molecular Operating Environment in order to evaluate their binding abilities with the corresponding protein kinase. Results: A series of 5-amino-1H-pyrazole-1-carbonyl derivatives have been designed and synthesized, screened for their inhibitory activities against FGFRs and cancer cell lines. Most of the target compounds showed moderate to good anti-proliferate activities against the tested enzymes and cell lines. The most promising compounds 8e suppressed FGFR1-3 with IC50 values of 56.4, 35.2, 95.5 nM, and potently inhibited the SNU-16 and MCF-7 cancer cells with IC50 values of 0.71 1.26 μM, respectively. And 8e inhibited the growth of cancer cells containing FGFR activated by multiple mechanisms. In addition, the binding interactions were quite similar in the molecular models between generated compounds and Debio-1347 with the FGFR1. Conclusion: According to the experimental findings, 5-amino-1H-pyrazole-1-carbonyl might serve as a promising template of an FGFR inhibitor.

Background: Development of potential antimicrobial agents is the main aim in the drug discovery process to overcome the problem of drug resistance. Pyrazolines and thiazolinones are extensively used as building blocks for the synthesis of diverse and medicinally important compounds. Methods: In this present work, a new series of functionalized pyrazolinyl-thiazolinone biheterocycles is designed and synthesized from N-pyrazolinecarbothioamide. Antimicrobial screening is carried out in order to discover their potential towards six bacterial and four fungal strains. The zone of inhibition (ZI in mm) was determined by the disc diffusion method and minimum inhibitory concentration (MIC in μg/mL) by macro dilution method. The druggability of these new entities is done through in silico pharmacokinetic profiling using Maestro 2017-1 interface of Schrödinger software. Results and Disscusion: Compounds 4c and 4e with chloro and iodo substituents on Nphenylacetamide ring displayed good inhibitory antibacterial activity against the tested bacterial strains with minimum MIC values when compared to the reference drug tetracycline. Compound 3 with an acetic acid derivative showed high antifungal activity among all the tested derivatives. Compound 3 not only showed antifungal activity but also qualified druggability test with no violation of Lipinski rule of five. Conclusion: The capability of the synthesized pyrazolinyl-thiazolinone derivatives was performed to efficiently inhibit the growth of microorganisms against selected bacterial and fungal strains. Further, these compounds are found to be effectively bound to the active sites of attractive target Escherichia coli FabH.

Background: Human mitotic kinesins play an essential role in mitotic cell division. Targeting the spindle separation phase of mitosis has gained much attention in cancer chemotherapy. Spindle segregation is carried out mainly by the kinesin, Eg5. Many Eg5 inhibitors are in different phases of clinical trials as cancer drugs. This enzyme has two allosteric binding sites to which the inhibitors can bind. The first site is formed by loop L5, helix α2 and helix α3 and all the current drug candidates bind un-competitively to this site with ATP/ADP. The second site, formed by helix α4 and helix α6, which has gained attention recently, has not been explored well. Some inhibitors that bind to this site are competitive, while others are uncompetitive to ATP/ADP. Phenylpropanoids are pharmacologically active secondary metabolites. Methods: In this study, we have evaluated fourteen phenyl propanoids extracted from Citrus medica for inhibitory activity against human mitotic kinesin Eg5 in vitro steady-state ATPase assay. Ther interactions and stability using molecular docking and molecular dynamics simulations. Results and Discussions: Of the fourteen compounds tested, naringin and quercetin showed good activity with IC50 values in the micromolar range. Molecular docking studies of these complexes showed that both the molecules interact with the key residues of the active site predominantly thorough hydrophobic & aromatic π–π interactions consistent with the known inhibitors. Besides, these molecules also form hydrogen bonding interactions stabilizing the complexes. Molecular dynamics simulations of these complexes confirm the stability of these interactions. Conclusion: These results can be used as a strong basis for further modification of these compounds to design new inhibitors with higher potency using structure-based drug design.

Background: In recent years, cancer has become the main cause of death and it is a serious threat to human health, so the development of new, selective and safe anticancer drugs is still the focus of medical research. Matrix metalloproteinases-2 (MMP-2) has been determined to play an important role in the regulation of tumor angiogenesis, which is closely related to the development of the tumor. Therefore, MMP-2 is considered as a promising target for tumor therapy. In this study, Tomper comparative molecular field analysis (Topomer CoMFA) and molecular docking were used to investigate the important role of sulfonamide hydroxamate derivatives, an inhibitor of MMP-2, in the inhibition of angiogenesis. Methods: Quantitative structure active relationship (QSAR) models of 35 sulfonamide hydroxamate derivatives with inhibitory MMPs were developed. The quantitative structure-activity relationship (QSAR) model was built by using Topomer comparative molecular field analysis (Topomer CoMFA) technique. Results and Discussions: The results show that the cross-validated q2 value of the Topomer CoMFA model is 0.881 and the non-cross-validated r2 value is 0.967. The results show that the model is reasonable and reliable, and has good prediction ability. Molecular docking studies were used to find the actual conformations of chemicals in active sites of cancer protease, as well as the binding mode pattern to the binding site in MMP-2. The information provided by the 3D-QSAR model and molecular docking may lead to a better understanding of the structural requirements of 35 sulfonamide hydroxamate derivatives and help to design potential anti-cancer protease inhibitor molecules. Conclusion: Thirty-five analogs were used in the 3D-QSAR study. Topomer CoMFA 3D-QSAR method was used to build the model, and the model was well predicted and statistically validated. The results of 3D-QSAR and molecular docking analysis provide theoretical guidance for the synthesis of new MMP-2 inhibitors.

Background: Benzimidazole derivatives are an important class of heterocyclic compounds in organic chemistry as they are related to a wide range of biological properties, including antimicrobial activity. Methods: A series of 1-naphthoyl and benzoyl benzimidazole derivatives were synthesised, identified and screened for their antimicrobial activities against a number of different test organisms such as Escherichia coli, Pseudomonas aureginosa, Klebsiella pneumoniae, Staphylococcus aureus, Enterococcus faecalis, Bacillus cereus, Salmonella typhimurium, Candida albicans (yeast). Results and Discussion: Benzimidazole derivatives (3a-d) were synthesised by using 4 different aminoacids. L-methionine, L-isoleucine, D-Phenylysine and L-Phenylamine as starting materials in the study. Experimental studies involve the use of benzimidazole derivatives (3a-d) of the selected amino acids to synthesize the benzoyl and naphthoyl derivatives of benzimidazole (4a-d, 5a-c). The structures of the synthesized compounds were confirmed by spectroscopic analyses (FTIR, 1HNMR, 13C-NMR) and elemental analysis. Conclusion: In this study, only one compound (5a) showed a low MIC value against the eukaryotic microorganism C. albicans. The other six compounds showed higher antimicrobial activities against the prokaryotes C. albicans which is a normal flora in the mouth but is one of the organisms that cause infections leading to the weakening of the human immune system. Compound 5a is a candidate for future alternative antimicrobial drugs against C. albicans infections. In addition, compound 5a has a potential to be used as an inhibitor against P. aureginosa for the treatment of cystic fibrosis.

Background: Akt is overexpressed or activated in a variety of human cancers, including gliomas, lung, breast, ovarian, gastric and pancreatic carcinomas. Akt inhibition leads to the induction of apoptosis and inhibition of tumor growth and therefore extensive efforts have been devoted to the discovery of potent antitumor drugs targeting Akt. Objectives: The objective of this work was to identify potent anticancer agents targeting Akt. Methods: New hydrazone derivatives were synthesized and investigated for their cytotoxic effects on 5RP7 H-ras oncogene transformed rat embryonic fibroblast and L929 mouse embryonic fibroblast cell lines. Besides, the apoptotic effects of the most active compounds on 5RP7 cell line were evaluated using flow cytometry. Their Akt inhibitory effects were also investigated using a colorimetric assay. In silico docking and Absorption, Distribution, Metabolism and Excretion (ADME) studies were also performed using Schrödinger’s Maestro molecular modeling package. Results and Discussion: Compounds 3a, 3d, 3g and 3j were found to be effective on 5RP7 cells (with IC50 values of <0.97, <0.97, 1.13±0.06 and <0.97 μg/mL, respectively) when compared with cisplatin (IC50= 1.87±0.15 μg/mL). It was determined that these four compounds significantly induced apoptosis in 5RP7 cell line. Among them, N'-benzylidene-2-[(4-(4-methoxyphenyl)pyrimidin- 2-yl)thio]acetohydrazide (3g) significantly inhibited Akt (IC50= 0.5±0.08 μg/mL) when compared with GSK690693 (IC50= 0.6±0.05 μg/mL). Docking studies suggested that compound 3g showed good affinity to the active site of Akt (PDB code: 2JDO). According to in silico ADME studies, the compound also complies with Lipinski's rule of five and Jorgensen's rule of three. Conclusion: Compound 3g stands out as a potential orally bioavailable cytotoxic agent and apoptosis inducer targeting Akt.

Aims: To find out Potential Drug targets against HPV E7. Background: Oncoprotein E7 of Human Papilloma Virus (HPV-16), after invading human body alter host protein-protein interaction networks caused by the fluctuations of amino acid residues present in E7. E7 interacts with Rb protein of human host with variable residual fluctuations, leading towards the progression of cervical cancer. Objective: Our study was focused our computational analysis of the binding and competing interactions of the E7 protein of HPV with Rb protein. Methods: Our study is based on analysis of dynamic fluctuations of E7 in host cell and correlation analysis of specific residue found in motif of LxCxE, that is the key region in stabilizing interaction between E7 and Rb. Results and Discussions: Cysteine, Leucine and Glutamic acid have been identified as hot spot residues of E7 which can provide platform for drug designing and understanding of pathogenesis of cervical cancer, in future. Our study shows validation of the vitality of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer. Conclusion: Our study shows validation of the vitality of linear binding motifs LxCxE of E7 of HPV in interacting with Rb as an important event in propagation of HPV in human cells and transformation of infection into cervical cancer. Other: E7 interacts with Rb protein of human host with variable residual fluctuations, leading towards the progression of cervical cancer.

Background: Hepatocellular carcinomas (HCCs) are inherently chemotherapy-resistant tumors with about 30-50% activation of PI3K/Akt/mTOR pathway, and this pathway is not aberrant in normal cells. Therefore, targeting the PI3K/Akt/mTOR pathway has become a promising strategy in drug designing to combat liver cancer. Recently, many studies with phytochemicals suggest few classes of compounds, especially flavonoids, to be useful in down-regulating the PI3K/Akt/mTOR pathway corresponding to HCC. In the present study, an attempt is made to explore flavonoids, from which the best mTORC1 inhibitor against hepatocellular carcinoma is selected using computational molecular modeling. Methods: In the present study, we performed a virtual screening method with phytochemicals of flavonoid category. To ensure proper bioavailability and druggability, pharmacokinetic and interaction parameters have been used to screen the molecules. The target protein molecules have been selected from the RCSB. The interaction studies have been conducted using Biovia Discovery Studio client version 17.2.0.1.16347 and the pharmacokinetic predictions have been made through ADMET SAR. The responsiveness towards the regulation of the mTOR pathway varies from person to person, demanding a pharmacogenomic approach in the analysis. The genetic variants (Single Nucleotide Variants-SNVs) corresponding to the mutations have been identified. Results and Discussions: The study identified phytoconstituents with better interaction with receptor FKBP12, a Rapamycin binding domain which is the target of Rapamycin and its analogues for mTORC1 inhibition in HCC. Another protein, ‘AKT serine/threonine-protein kinase’ has been identified, which is associated with activation of mTORC1. The molecular interaction studies (docking studies) and ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis were used to identify the affinity between selected phytoconstituents as mTORC1 inhibitor against Hepatocellular carcinoma. The docking studies support Kaempferol to be a potential ligand with docking score values of 33.4 (3CQU-3D structure of AKT1)] and 27.3 (2FAP-3D structure of FRB domain of mTOR) respectively as compared to that of standard drug Everolimus with 24.4 (3CQU-3D structure of AKT1) and 20.1 (2FAP-3D structure of FRB domain of mTOR) respectively. Docking studies along with ADMET results show that Kaempferol has favorable drug likeliness properties and binds to the same active site (site1) of the targeted proteins (3CQU-3D structure of AKT1) and (2FAP-3D structure of FRB domain of mTOR) where the standard drug Everolimus is known to bind. Conclusion: The study exhibited that Kaempferol had a better binding affinity towards the receptor FKBP12, a Rapamycin Binding Domain and AKT serine/threonine-protein kinase resulting in its better efficacy in the mTORC1 inhibition as when compared with standard drug Everolimus against HCC. To the best of our knowledge, no studies have been reported on Kaempferol as mTORC1 inhibitor against Hepatocellular carcinoma.

Background: Dapagliflozin, developed as an SGLT-2 inhibitor, has a low melting point and high hygroscopicity, which needs extreme care during pharmaceutical production to keep the active pharmacological property. Various attempts have been made to overcome these problematic properties. Objectives: To develop dapagliflozin prodrugs that have similar pharmacological effects with improved hygroscopicity and thermal stability. Methods: The novel dapagliflozin ester prodrugs containing pharmaceutically acceptable moieties were synthesized and their pharmacokinetics (PK) and physical properties were compared with dapagliflozin propanediol hydrate (DPD, Farxiga®). The PK in dog and rat, in vitro stability, hygroscopicity, and physical property studies in accelerated conditions (40°C, 75% RH) were performed with prodrugs. Results and Discussions: Among the eight synthesized prodrugs, Cmax and AUC0-48h values of prodrug 8b (1.35 μg/ml and 14.78 μg·h/ml, respectively) were similar to those of DPD (1.67 μg/ml and 14.27 μg·h/ml, respectively). However, the rest of the prodrugs 8a, 8c, 8d, 8e, 8f, 8g and 8h showed significantly lower Cmax and AUC0-48h values than DPD. Prodrug 8b completely converted into parent drug in the body. Conclusion: The novel prodrug 8b exhibited comparative PK profile to that of DPD, but with low hygroscopic property and better thermal stability than DPD.

Background: Mycobacterium tuberculosis is a causative agent of tuberculosis. It is a non-motile, acid-fast, obligatory aerobic bacterium. Finding novel drug targets in Mycobacterium tuberculosis has become extremely important as the bacterium is evolving into a more dangerous multi-drug resistant pathogen. The predominant strains in India belong to the Central-Asian, East- African Indian, and Beijing clad. For the same reason, the whole proteomes of a non-virulent strain (H37Ra), a virulent (H37Rv) and two clinical strains, a Central-Asian clad (CAS/NITR204) and a Beijing clad (CCDC5180) have been selected for comparative study. Selecting a phylogenetically close and majorly studied non-virulent strain is helpful in removing the common and undesired proteins from the study. Objective: The study compares the whole proteome of non-virulent strain with the other three virulent strains to find a unique protein responsible for virulence in virulent strains. It is expected that the drugs developed against identified targets will be specific to the virulent strains. Additionally, to assure minimal toxicity to the host, we also screened the human proteome. Methods: Comparative proteome analysis was used for target identification and in silico validation of identified target protein Rv2466c, identification of the respective ligand of the identified target protein and binding interaction study using Molecular docking and Molecular Dynamic Simulation study were used in this study. Result and Discussions: Finally, eleven proteins were found to be unique in virulent strain only and out of which, Rv2466c (PDB-ID: 4ZIL) was found to be an essential protein and identified as a putative drug target protein for further study. The compound glutathione was found to be a suitable inhibitor for Rv2466c. In this study, we used a comparative proteomics approach to identify novel target proteins. Conclusion: This study is unique as we are assured that the study will move forward the research in a new direction to cure the deadly disease (tuberculosis) caused by Mycobacterium tuberculosis. Rv2466c was identified as a novel drug target and glutathione as a respective ligand of Rv2466c. Discovery of the novel drug target as well as the drug will provide a solution to drug resistance as well as the infection caused by Mycobacterium tuberculosis.

Background: Literature survey has pointed out that Benzimidazoles represent an interesting class of anthelmintics, of which several potent members were developed. Objective: Benzimidazoles hybridized with pharmacophoric moieties possessing anthelmintic activity were designed, synthesized to be evaluated against cercaria. Methods: Structural modification was achieved through 2- and 5-positions. Moreover, an in vitro cercarial assay was adopted to evaluate target compounds. Results and Discussions: Biological screening revealed that compound 3h showed significant activity with a survival index of 35% at a 100 μg/mL concentration. Whereas, compounds 3a and 3c showed moderate activity, the rest of the tested compounds exhibited low activity. Conclusion: The current study evidenced that the new hybrids "benzimidazole-thiophen-aryl" are successful as cercacidal agents. Further studies of this novel tri-ring system are suggested on adult worms of S. mansoni.

Background: Inhibition of cancer cell growth and low in vivo toxicity are two important criteria for the development of anti-cancer drugs. Curcumin is a promising candidate for developing novel anti-cancer drug analogs. The research group designed the 3,5-bis-(3,4,5- trimethoxybenzylidene)-1-methyl-piperidin-4-one analog of curcumin that significantly inhibited the growth of esophageal cancer cells in vivo. In this study, 81 curcumin analogs were synthesized, analyzed both in vitro and in vivo, and their structure activity relationships (SARs) were determined. Methods: Based on the parent structure of curcumin, 81 analogs of 3,5-bis(substitutedbenzylidene)- piperidin-4-one compounds were designed and synthesized. Their anti-cancer activity in the human cancer cell lines was evaluated using the MTT assay, and in vivo toxicity was evaluated in mice. The SARs of selected compounds were analyzed. Results and Discussion: Among the designed curcumin analogs, 61 compounds exerted anti-cancer effects higher than the parent compound in vitro; 23 compounds inhibited cell growth in the human cancer cell line at low concentrations (IC50 values below 1 μM). The acute toxicity of curcumin analogs was tested in mice; 13 compounds were selected, which did not show any obvious toxicity at doses as high as 25.0 mg/kg. The SARs of these shortlisted curcumin analogs were determined. Conclusion: Twenty-three curcumin analogs exhibiting promising in vitro anti-cancer activity and low in vivo toxicity were designed. SAR analysis indicated the optimal functional groups in the molecule required for anti-cancer activity. This study not only suggested a useful strategy to design curcumin analogs for the development of anti-cancer drugs, but also revealed a group of curcumin analogs which could be further explored.