Letters in Drug Design & Discovery - Volume 19, Issue 4, 2022

Background: Natural products (NPs) are important sources for the design of new drugs and agrochemicals. Neopeltolide, a marine NP, has been identified as a potent Qo-site inhibitor of cytochrome bc1 complex. Methods: In this study, a series of neopeltolide derivatives was designed and synthesized by the simplification of its 14-membered macrolactone ring with a diphenyl ether fragment. The enzymatic inhibition bioassays and mycelium growth inhibition experiments against a range of fungi were performed to determine their fungicidal activities. Results: The derivatives have potent activity against the porcine bc1 complex. Compound 8q showed the best activity with an IC50 value of 24.41 nM, which was 8-fold more effective than that of positive control azoxystrobin. Compound 8a exhibited a 100% inhibitory rate against Zymoseptoria tritici and Alternaria solani at a 20 mg/L dose. Conclusion: Computational results indicated that compounds with suitable physicochemical properties, as well as those forming a hydrogen bond with His161, would have good fungicidal activity. These data could be useful for the design of bc1 complex inhibitors in the future.

Background: Cystic Fibrosis (CF) is a genetic disease, which has no effective treatment. Objective: The aim of our research is to predict the EC50 value of 2,3,4,5-tetrahydro-1H-pyrido[4,3- b]indole core as a novel chemotype of potentiators to establish a highly predicting quantitative structureactivity relationship model. Methods: 41 products were optimized, and a linear model was built by a heuristic method in CODESSA program. In this study, 3 descriptors were selected and utilized to build a nonlinear model in gene expression programming. Results: The square of the correlation coefficient of the heuristic method is 0.57, and the s2 is 0.30. In gene expression programming, the square of correlation coefficient and the mean square error for the training set are 0.74 and 0.13, respectively. The square of correlation coefficient and the mean square error for the test set are 0.70 and 0.27, respectively. Conclusion: The GEP model has stronger predictive ability to help develop the novel structure of 2,3,4,5- tetrahydro-1H-pyrido[4,3-b]indole of cystic-brosis-transmembrane conductance-regulator gene potentiators.

Background: Inflammation is a critical component of many disease progressions, such as malignancy, cardiovascular and rheumatic diseases. The inhibition of inflammatory mediators synthesis by modulation of cyclooxygenase (COX) and lipoxygenase (LOX) pathways provides challenging strategy for development of more effective drugs. Objective: The aim of this study was to design dual COX-2 and 5-LOX inhibitors with iron-chelating properties using a combination of ligand-based (three-dimensional quantitative structure-activity relationship (3D-QSAR)) and structure-based (molecular docking) methods.. Methods: The 3D-QSAR analysis was applied on a literature dataset consisting of 28 dual COX-2 and 5- LOX inhibitors in Pentacle software. The quality of developed COX-2 and 5-LOX 3D-QSAR models were evaluated by internal and external validation methods. The molecular docking analysis was performed in GOLD software, while selected ADMET properties were predicted in ADMET predictor software. Results: According to the molecular docking studies, the class of sulfohydroxamic acid analogues, previously designed by 3D-QSAR, were clustered as potential dual COX-2 and 5-LOX inhibitors with ironchelating properties. Based on the 3D-QSAR and molecular docking, 1j, 1g and 1l were selected as the most promising dual COX-2 and 5-LOX inhibitors. According to the in silico ADMET predictions, all compounds had ADMET_Risk score less than 7 and CYP_Risk score lower than 2.5. Designed compounds were not estimated as hERG inhibitors and 1j had improved intrinsic solubility (8.704) in comparison to the dataset compounds (0.411-7.946). Conclusion: By combining 3D-QSAR and molecular docking, three compounds (1j, 1g and 1l) were selected as the most promising designed dual COX-2 and 5-LOX inhibitors, for which good activity, as well as favourable ADMET properties and toxicity, are expected.

Background: Breast cancer is most commonly reported to contribute to people's death. Nowadays, cancer treatment is focused on investigating anticancer drugs from natural compounds. Various methods, including in vitro, in vivo, and in silico methods, are used to assess the potential of anticancer compounds. The efficacy of bioactive compounds from medicinal plant origin lies in their affordability and minimized side effects. The Garcinia genus contains bioactive compounds, such as xanthones, benzophenones, triterpenes, biflavonoids, and benzoquinones. Objective: The study aimed at investigating an active compound that can inhibit cancer cell growth and proteins that contribute to cancer cell growth, such as Caspase-9, TNF-α, ER-α, and HER-2. Methods: This study is divided into three steps. The first step is the isolation of the active compound from G. cymosa. The second step is an assessment of cytotoxic activity against MCF-7 cell by using MTT assay, and the last one is an investigation of the molecular mechanism of an active compound against Caspase-9, TNF-α, ER-α, and HER-2 by using in silico studies utilizing various programs, such as PyRx 0.8, PYMOL, and Discovery Studio. Results: Morelloflavone from G. cymosa stem barks has exhibited anticancer activity (55.84 μg/mL) eight times lower than doxorubicin (6.99 μg/mL), but it can block the activity of Caspase-9, TNF-α, ER- α, and HER-2. The binding affinity of morelloflavone is the strongest of all ligands. Conclusion: The natural flavonoid, morelloflavone, may be a new lead candidate for anticancer agent inhibiting action mechanism of Caspase-9, TNF-α, ER-α, and HER-2, respectively.

Background: As an opportunistic pathogen, Pseudomonas aeruginosa causes many different hazardous infections. The high mortality rate resulting from infection with this antibiotic-resistant pathogen has made it a major challenge in clinical treatment; it has been listed as the most harmful bacterium to humans by the WHO. So far, no vaccine has been approved for P. aeruginosa. Objective: Infections performed by bacterial attachment and colonization with type IV pili (T4P), known as the most essential adhesive vital for adhesion, while pilQ is necessary for the biogenesis of T4P, also outer membrane proteins of a pathogen is also effective in stimulating the immune system; in this regard, pilQ, OprF, and OprI, are excellent candidate antigens for production of an effective vaccine against P. aeruginosa. Methods: In this research, various bioinformatics methods were employed in order to design a new multiepitope peptide vaccine versus P. aeruginosa. Since T CD4+ cell immunity is important in eradicating P. aeruginosa, OprF, OprI, and pilQ antigens were analyzed to determine Helper T cell Lymphocyte (HTL) epitopes by many different immunoinformatics servers. One of the receptor agonists 2 (TLR2), a segment of the Por B protein from Neisseria meningitides was used as an adjuvant in order to stimulate an effective cellular immune response, and suitable linkers were used to connect all the above mentioned parts. In the vaccine construct, linear B cell epitopes were also identified. Results: Conforming the bioinformatics forecasts, the designed vaccine possesses high antigenicity and is not allergen. Conclusion: In this regard, the designed vaccine candidate is strongly believed to possess the potential of inducing cellular and humoral immunity against P. aeruginosa.

Background: Pemigatinib (INCB054828) and Infigratinib (BGJ398) are the few selective drugs that are approved by the FDA to treat cholangiocarcinoma, a rare form of bile duct cancer. Infigratinib is a pan FGFR inhibitor and has been found promising in Phase-3, first-line PROOF clinical trial. So, screening drug-like compounds having similar pharmacophoric features like infigratinib is the inspiration of the present work. Objective: The objective was to identify drug-like compounds with similar pharmacophoric features as in infigratinib. The compounds screened through the 3D query pharmacophore of infigratinib were also predicted for ADMET properties so that the compounds may have good bioavailability. Methods: A pharmacophore was generated from the crystal structure of infigratinib with several pharmacophoric features such as hydrogen bond donor, hydrophobic, positive ionizable, and ring aromatic. MayBridge database containing 65,263 compounds was used for virtual screening (VS) using LibDock. The initial Hit compounds were subjected to ADMET predictions. Finally, two Hit compounds were selected and docked with the FGFR-1 receptor to predict the interaction of the ligand atoms with the amino acid residues of the receptor's active site. Results: The fit score for infigratinib, N-(4-fluorophenyl)-2-(5-((2-(4-methoxy-2,5-dimethylphenyl)-2- oxoethyl)thio)-4-methyl-4H-1,2,4-triazol-3-yl)acetamide (Hit-1) and 4-(4-((2-(5,6-dimethyl-1H-benzo[d] imidazol-2-yl)ethyl)carbamoyl)pyridin-2-yl)-1-methylpiperazin-1-ium (Hit-4) is 4.58901, 4.36649, and 3.71732, respectively. The LibDock score of infigratinib, Hit-1, and Hit-4 is 122.474, 123.289, and 123.353, respectively. The binding affinity score (-PLP1) of infigratinib, Hit-1, and Hit-4 is -143.19, - 102.72, and -91.71. Conclusion: The present study concluded that the two compounds designated as Hit-1 and Hit-4 have been identified as binders of FGFR-1, and Hit-4 occupies the whole pharmacophoric space of infigratinib, and both the compounds LibDock scores are better than the infigratinib. The two compounds Hit-1 and Hit-4 may be synthesized and studied for their enzyme inhibition assay on FGFR-1 and biologically evaluated on different cell lines for Cholangiocarcinoma.

Background: Cardiovascular Diseases (CVDs) remain the leading cause of death worldwide, which urges for effective strategies of prevention and treatment. Withaferin-A (WFA), the key metabolite identified in Withania somnifera, has been known for its cardioprotective properties. Although it has been traditionally employed to treat cardiovascular ailments for several decades, its exact mechanism of action still remains unexplained. Objective: The current study modeled and scored the interactions of WFA with nine prospective protein targets associated with cardiovascular diseases through molecular docking and DSX-scoring. Methods: Molecular docking was carried out using Autodock and DSX scoring was carried out using DSX standalone software. WFA was observed to favorably interact with six targets before DSX-based rescoring, but only with Poly (ADP-Ribose) Polymerase-1 and P2Y Purinoceptor-1 after DSX-based rescoring. The spatial orientation, physicochemical properties and structural features of Withaferin-A were compared with that of the approved drugs by pharmacophore modeling and hierarchical clustering. Results: The results of molecular docking, DSX-based rescoring and complete pharmacophore modeling together revealed that PARP1 and P2Y1 receptors could be prospective targets of WFA for the treatment of CVD. Conclusion: Simulation using GROMACS has revealed that WFA forms a more stable complex with PARP1 and will be useful in developing broad-spectrum drugs against cardiovascular diseases. Further computational studies through machine learning and network pharmacology methods can be carried out to improve the Withaferin-A compound features by incorporating additional functional groups necessary for molecular recognition of the target genes in the network responsible for cardiovascular diseases.

Background: DNA gyrase subunit B (1KZN) is an attractive target for antibacterial drug development because of its role in DNA replication. The fast development of antimicrobial medication resistance necessitates the quick discovery of new antimicrobial medicines. Objective: The goal of this research was to design, synthesize, and discover benzo-fused five-membered nitrogen-containing heterocycles that bind to DNA gyrase subunit B via molecular docking (1KZN). Methods: Based on literature research, 2-(1H-1,2,3-Benzotriazol-1-yl)-N-substituted acetamide was synthesized using an efficient method. All synthesized compounds were evaluated for antibacterial activity against three distinct organisms: E. coli, Pseudomonas aeruginosa, Staphylococcus aureus. Results: In a docking investigation, the chemical interacts with the active site of DNA gyrase subunit B (1KZN), indicating that it might have antibacterial action. Conclusion: According to the findings of this research, the compounds 3d and 3f showed antibacterial properties. For Staphylococcus aureus, 3c has the potential to be an antibacterial agent.

Background: Type 2 diabetes mellitus (T2DM), which is the epidemic of the 21st century, has affected millions of people worldwide. Traditional methods available for the treatment are associated with various side effects. Among the newer therapies, DPP-4 (Dipeptidyl peptidase-4) inhibition has been a promising therapy for the past decade with the scope of further development, especially in peptidomimetics. Objective: 5(S)-methyl-L-proline containing peptidomimetic compounds were designed in the previous work. The designed compounds were synthesized and characterized by spectral methods, such as mass spectrometry, ¹H NMR, and ¹³C NMR (Nuclear magnetic resonance) spectroscopy. The purity of the final compounds was determined by high-performance liquid chromatography (HPLC). The synthesized compounds were in vitro evaluated for their DPP-4 inhibitory activity. Methods: Compounds were peptide in nature and were synthesized using the conventional synthesis approach, where peptide synthesis was done using an acid-amine coupling reagent. They were evaluated through fluorimetric enzyme-based assay using a DPP-4 inhibitor screening kit. Moreover, the CLARIOstar microplate reader instrument was used to measure fluorescence. Results: 5(S)-methyl-L-proline containing 13 compounds were synthesized. All of them were characterized for structural integrity using spectral methods. They had HPLC purity of more than 95% and were evaluated for DPP-4 inhibition. Compounds 1, 7, 10, 11, 14 and 17 were found to have good inhibition than others. These compounds were further evaluated at different concentrations to develop a linear correlation coefficient (R²). Conclusion: Six compounds were found to have good DPP-4 inhibition, hence it further opens the possibility of developing DPP-4 inhibitor-containing 5(S)-methyl-L-proline.