Letters in Drug Design & Discovery - Volume 18, Issue 5, 2021

The recent pandemic caused by a novel coronavirus known as SARS-CoV-2 has caught the international community by surprise. There is still no effective vaccine or treatment option against this virus. In this perspective, we discussed the potential protective and therapeutic effects of chitosan, as an FDA-approved biomolecule, against COVID-19 and influenza viruses.

Background: Tamoxifen (TAM), a non-steroidal antiestrogen, constitutes the endocrine treatment of choice against breast cancer. Since its inauguration, substantial effort has been devoted towards the design and synthesis of TAM’s analogues aiming to improve its bioactivity and reveal their structure-activity relationship. Objective: One of the most studied synthetic features of TAM’s structure is the ether side chain, which is strongly related to its positioning into the active site of the Estrogen Receptors (ERα and ERβ). Herein, we present the application of a straightforward route for the efficient synthesis of selected novel carbamoyloxy analogues of TAM and the evaluation of their respective binding affinities to the Estrogen Receptors α and β. Methods: A one-pot reaction was applied for the construction of TAM’s triarylethylene core moiety, which subsequently was derivatized to provide efficiently the target carbamoyloxy analogues of TAM. The Z and E isomers of the latter were separated using RP-HPLC-UV and their binding affinities to ERα and ERβ were measured. Results: Among all compounds synthesized, the dimethyl derivative was determined as the most potent for both receptors, displaying binding affinity values comparable to TAM, though the Zdiethyl analogue maintained substantial affinity to both ERs. The aforementioned results were further studied by theoretical calculations and molecular modelling to delineate a concordance among calculations and biological activity. Conclusion: Approach applied herein permitted the extraction of a useful structure-activity relationship correlation pattern highlighting the importance of a chemically stabilized tamoxifen side chain.

Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a novel member of the genus betacoronavirus in the Coronaviridae family. It has been identified as the causative agent of coronavirus disease 2019 (COVID-19), spreading rapidly in Asia, America and Europe. Like some other RNA viruses, RNA replication and transcription of SARS-CoV-2 rely on its RNA-dependent RNA polymerase (RdRP), which is a therapeutic target of clinical importance. Crystal structure of SARS-CoV-2 was solved recently (PDB ID 6M71) with some missing residues. Objective: We used SARS-CoV-2 RdRP as a target protein to screen for possible chemical molecules with potential anti-viral effects. Methods: Here we modelled the missing residues 896-905 via homology modelling and then analysed the interactions of Hepatitis C virus allosteric non-nucleoside inhibitors (NNIs) in the reported NNIs binding sites in SARS-CoV-2 RdRP. Results: We found that MK-3281, filibuvir, setrobuvir and dasabuvir might be able to inhibit SARS-CoV-2 RdRP based on their binding affinities in the respective binding sites. Conclusion: Further in vitro and in vivo experimental research will be carried out to evaluate their effectiveness in COVID-19 treatment in the near future.

Background: α-Glucosidase inhibitors have occupied a significant position in the treatment of type 2 diabetes. In this respect, the development of novel and efficient non-sugar-based inhibitors is in high demand. Objective: Design and synthesis of new 5-arylisoxazole-1,3,4-thiadiazole hybrids possessing α- glucosidase inhibitory activity were developed. Methods: Different derivatives were synthesized by the reaction of various 5-arylisoxazole-3- carboxylic acids and ethyl 2-((5-amino-1,3,4-thiadiazol-2-yl)thio)acetate. Finally, they were evaluated for their α-glucosidase inhibitory activity. Results: It was found that ethyl 2-((5-(5-(2-chlorophenyl)isoxazole-3-carboxamido)-1,3,4-thiadiazol- 2-yl)thio)acetate (5j) was the most potent compound (IC50 = 180.1 μM) compared with acarbose as the reference drug (IC50 = 750.0 μM). Also, the kinetic study of 5j revealed a competitive inhibition and docking study results indicated desired interactions of that compound with amino acid residues located close to the active site of α-glucosidase. Conclusion: Good α-glucosidase inhibitory activity obtained by the title compounds introduced them as an efficient scaffold, which merits to be considered in anti-diabetic drug discovery developments.

Background: The genus Morus is one of the rich sources of phytomedicine and considered a beneficial natural source for drugs with potential antimicrobial effect under the traditional system of medicine. Introduction: In the present study, three bioactive compounds isolated from the leaves of two species of genus Morus and their antibacterial effect against selective pathogens were assessed. Methods: The inhibitory effects of the three molecules isolated were assessed for their minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) against selected pathogens. The in-silico studies provided the toxicity profile and the binding interactions with glucosamine- 6-phosphate synthase for all the isolates. Results: Among the three compounds tested, cathafuran-B showed a prominent bacteriostatic and bactericidal effect, which is supported by the results of in-silico analysis suggesting that cathafuran- B could be a potential glucosamine-6-phosphate synthase inhibitor. Conclusion: The biomolecule isolated from less explored Morus laevigata exhibiting higher antibacterial effect among the compounds tested warranted opening a new prospect in phytomedicinal research for exploring its pharmacological properties and lowering the utilization load present on highly explored Morus alba.

Background: Stenotrophomonas maltophilia is an aerobic, non-fermentative, gram negative, multidrug resistant and opportunistic nosocomial pathogen. It is associated with high morbidity and mortality in severely immunocompromised paediatric patients, including neonates. Immunoinformatic analysis paved a new way to design epitope-based vaccines which resulted in a potential immunogen with advantages such as lower cost, specific immunity, ease of production, devoid of side effects, and less time consumption than conventional vaccines. Till date, there is no development in the vaccines or antibody-based treatments for S. maltophilia-associated infections. Introduction: Currently, epitope-based peptide vaccines against pathogenic bacteria have grasped more attention. In our present study, we have utilized various immunoinformatic tools to find a prominent epitope that interacts with the maximum number of HLA alleles and also with the maximum population coverage for developing a vaccine against Stenotrophomonas maltophilia. Methods: This study has incorporated an immunoinformatic based screening approach to explore potential epitope-based vaccine candidates in Stenotrophomonas maltophilia proteome. In this study, 4365 proteins of the Stenotrophomonas maltophilia K279a proteome were screened to identify potential antigens that could be used as a good candidate for the vaccine. Various immunoinformatic tools were used to predict the binding of the promiscuous epitopes with Major Histocompatibility Complex (MHC) class I molecules. Other properties such as allergenicity, physiochemical properties, adhesion properties, antigenicity, population coverage, epitope conservancy and toxicity were analysed for the predicted epitope. Results: This study helps in finding the prominent epitope in Stenotrophomonas infections. Hence, the main objective in this research was to screen complete Stenotrophomonas maltophilia proteome to recognize putative epitope candidates for vaccine design. Using computational vaccinology and immunoinformatic tools approach, several aspects are obligatory to be fulfilled by an epitope to be considered as a vaccine candidate. Our findings were promising and showed that the predicted epitopes were non-allergenic and fulfilled other parameters required for being a suitable candidate based on certain physio-chemical, antigenic and adhesion properties. Conclusion: The epitopes LLFVLCWPL and KSGEGKCGA have shown the highest binding score of −103 and −78.1 kcal/mol with HLA-A*0201 and HLA-B*0702 MHC class I allele, respectively. They were also predicted to be immunogenic and non-allergenic. Further various immunological tests, both in vivo and in vitro methods, should be performed for finding the efficiency of the predicted epitope in the development of a targeted vaccine against Stenotrophomonas maltophilia infection.

Aims: In this study experiments were carried out to explore antioxidant, antimicrobial, cytotoxic properties of novel indole derivative 1-ethyl-2-phenyl-3-phenylethyl-3-thiophen-2-yl-1Hindole (EPI) together with its effect on glutathione S-transferases (GST) activities in human liver carcinoma (HepG2) cells. Background: Indoles probably represent one of the most important heterocyclic structures that have been attracting the interest of many scientists in drug discovery. Objective: The present study was carried out to explore antioxidant, antimicrobial, cytotoxic properties of novel indole derivative 1-ethyl-2-phenyl-3-phenylethyl-3-thiophen-2-yl-1H-indole (EPI) and its effect on glutathione S-transferases (GST) activities in human liver carcinoma (HepG2) cells. Materials and Methods: Pd-catalyst Sonogashira coupling reactions, MTT Assay, Antioxidant capacity test, Antimicrobial test, GST enzyme activity test. Results: 1-ethyl-2-phenyl-3-(phenylethynyl)-1H-indole had antioxidant and antimicrobial properties. It displayed significant induction in glutathione S-transferases (GST) enzyme activity in human liver cancer cell lines (HepG2), but cytotoxic effect on all tested cancer cell lines could not be observed. Conclusion: All of these results showed that 1-ethyl-2-phenyl-3-(phenylethynyl)-1H-indole had antioxidant and antimicrobial properties without cytotoxic effect, which could make it a promising active component with further studies.

Background: Dibenzofuran ring is a typical heterocyle that is found in many natural sources and its derivatives exhibit a wide scale of biological applications similar to its analog ring systems; furan and benzofuran. Materials and Methods: Novel N-(2-methoxydibenzofuran-3-yl)-2-aryloxyacetamide derivatives (2a-l) were synthesized and evaluated for their cytotoxic activity against A549 lung cancer and NIH/3T3 mouse embryofibroblast cell lines. The inhibition percentages of cathepsin D, L, acetylcholinesterase (AChE) and butrylcholinesterase (BuChE) enzymes provoked by the compounds were also determined. Results and Discussion: Most of the compounds exhibited significant cytotoxicity whose IC50 values were identified lower than the tested lowest concentration (<3.90 μg/mL). Compound 2i against cathepsin D and compound 2k against cathepsin L displayed the highest inhibitory activity. Regrettably, the compounds demonstrated very weak AChE and BuChE inhibition. Conclusion: Compounds 2b, 2c, 2e, 2i and 2k exhibited the highest antiproliferative activity against A549 cell lines with selective profile. However, they did not display satisfying results on tested enzymes.

Background: Abnormal deposition of amyloid beta (Aβ) is considered the primary cause of neurocognitive disorders (NCDs). Inhibiting cytotoxicity is an important aspect of the treatment of NCDs. Stachydrine (STA) has been widely used for gynecological and cardiovascular disorders. However, whether STA has protective functions in PC12 cells treated with Aβ25-35 remains unclear. Introduction: Traditional Chinese Medicine, stachydrine (STA), is a water-soluble alkaloid of Leonurus heterophyllus, which can inhibit cell apoptosis, suppress tumor growth, maintain homeostasis of myocardial cells, and alleviate endothelial dysfunction. This study will investigate the effect of STA on inhibiting PC12 cell apoptosis induced by Aβ25-35 in an in vitro cell model of neurocognitive disorders. Methods: The differentially expressed genes (DEGs) in cells treated with STA were analyzed according to the Gene Expression Omnibus (GSE) 85871 data, and the STITCH database was used to identify the target genes of STA. PC12 cells were treated with Aβ25-35 and/or STA, 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay was performed and lactate dehydrogenase (LDH) activity was determined. The cell cycle distribution was detected by flow cytometry, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) or Western blotting were used to detect the expression of genes or proteins. Results: GSE85871 data showed 37 upregulated and 48 downregulated genes among the DEGs affected by STA. The results from the STITCH database showed that RPS8 and EED were target genes of STA. GSE1297 analysis showed the 13 most significantly upregulated genes. STA might affect the occurrence of NCDs through the interaction of TP53 with EED and RPS8. Finally, Aβ25-35 promoted apoptosis and LDH release of PC-12 cells, arrested the cell cycle in the G2/M phase, and inhibited the expression of the RPS8, EED, Bcl-2 and P53 genes. STA could reverse the effect of Aβ25-35. Conclusion: STA may play an important role in inhibiting apoptosis induced by Aβ25-35 by targeting the RPS8 and EED genes in the NCDs model in vitro.

Background: Spirocyclic indoline compounds widely exist in numerous natural products and synthetic molecules with significant biological activities. In recent years, these kinds of compounds have attracted extensive attention as potent anti-tumor agents in the fields of pharmacology and chemistry. Objective: In this study, we focused on designing and synthesizing novel 1'-methylspiro[indoline- 3,4'-piperidine] derivatives, which were evaluated by preliminary bioactivity experiment in vitro and molecular docking. Materials and Methods: The key intermediate 1'-methylspiro[indoline-3,4'-piperidine] (B4) reacted with benzenesulfonyl chloride with different substituents under alkaline condition to obtain its derivatives (B5-B10). We evaluated their antiproliferative activities against A549, BEL-7402 and HeLa cell lines by MTT assay. We performed the CDOCKER module in Accelrys Discovery Studio 2.5.5 for molecular docking of compound B5, and investigated the binding modes of compound B5 with three different target proteins. Results: The results indicated that compounds B4-B10 exhibited good antiproliferative activities against the above three types of cell lines, in which compound B5 with chloride atom as electronwithdrawing substituent on a phenyl ring showed the highest potency against BEL-7402 cell lines (IC50=30.03±0.43 μg/mL). The results of molecular docking showed that the binding energies of the prominent bioactive compound B5 with CDK, c-Met, and EGFR protein crystals are -44.3583 kcal/mol, -38.3292 kcal/mol, -33.3653 kcal/mol, respectively. Conclusion: 1'-methylspiro[indoline-3,4'-piperidine] and its six derivatives were synthesized and evaluated against BEL-7402, A 549, and Hela cell lines. Compound B5 showed significant inhibition on BEL-7402 cell lines. Molecular docking assays revealed that B5 as a ligand showed strong affinity and appropriate binding pose on the amino acid residues in active sites of the tested targets, which encourage us to conduct further evaluation such as the kinase experiment.

Background: Thrombolysis and endovascular thrombectomy are the two main therapeutic strategies for ischemic stroke in clinic. However, reperfusion injury causes oxidative stress leading to overproduction of reactive oxygen species, mitochondrial dysfunction and subsequent cell death. Methods: We designed and synthesized two tetramethylpyrazine-nitrone derivatives (T-003 and T- 005) and investigated their abilities for scavenging free radicals and protective effects as well as neurite outgrowth promotion in vitro. Results: Both of them showed potent radical-scavenging activity and neuroprotective effects against iodoacetic acid-induced cell injury. Furthermore, T-003 and T-005 significantly promoted neurite outgrowth in PC12 cells. Conclusion: Our results suggest that compound T-003 and T-005 could be potent antioxidants for the treatment of neurological disease, particularly ischemic stroke.

Background: ALK inhibitors have become a plausible option for anticancer therapy with the availability of several FDA-approved molecules and clinical trial candidates. Hence, the design of new ALK inhibitors using computational molecular docking studies on the existing inhibitors, is an attractive approach for anticancer drug discovery. Methods: We generated six types of independent models through structural based molecular docking study, three-dimensional quantitative structure-activity relationship (3D-QSAR) study, and 2DQSAR approaches using different fingerprints, such as dendritic, linear, 2D molprint, and radial. Results: Comparison of the generated models showed that the hinge region hydrogen bond interacted with amino acids ASP1206, MET1199, and LYS1150 in docking analysis and the hydrophobic interacted with amino acids GLU1210, ARG1209, SER1206, and LYS1205 residues are responsible for the ALK inhibition. In the 3D-QSAR study, the hydrogen bond donor features of 2,4- diaryl aminopyrimidine substituents, isopropyl phenyl ring groups in hydrophobic features, and electron-withdrawing groups matched the generated contour plots. The 2D-QSAR fingerprint studies indicated that higher potency was associated with the 2-hydroxy-5-isopropyl benzamide functional group and substituted phenylamine at the second position of the pyrimidine group. Conclusion: We conclude that the incorporation of these functional groups in the design of new molecules may result in more potent ALK inhibitors.