Letters in Drug Design & Discovery - Volume 20, Issue 7, 2023

Background: Cancer is the world's second-largest cause of death, and is responsible for an estimated 9.6 million mortality cases in 2018. Poly-ADP-ribose polymerases (PARPs) are enzymes and a family of proteins involved in many cellular processes, including DNA repair, gene regulation, chromatin remodeling, and apoptosis. The first characterized and best-known member of the PARP family is poly(ADP-ribose) polymerase 1 (PARP-1). PARP-1 is a major protein for DNA single-strand breaks in the BER pathway (base excision repair) (SSBs). Objective: The objective of this article was to compile synthetic PARP-1 inhibitors reported in the last decade. Methods: In the present manuscript, bibliographic investigation was carried out by scrutinizing peerreviewed articles from online/offline databases. The inclusion criteria consisted of the most relevant studies indicating the relationship between PARP-1 and cancer in textbooks/edited books and peer-reviewed papers from scientific databases, like SCOPUS, PUBMED, NISCAIR, and Google Scholar since 2010 to 2020. Only the studies published in English language were searched/considered. The exclusion criteria consisted of the studies on other PARP isoforms than PARP-1. The studies thus obtained were classified according to the heterocyclic moieties, year of publication, etc. The data compiled in this article is a systematic review of the reported studies. Results: The literature reports indicated that a number of PARP-1 inhibitors reported have IC50 value in nanomolar concentration. Conclusion: PARP-1 is an essential target for anti-cancer drug discovery. Further research on more effective and safe PARP-1 inhibitors needs to be carried out, and we may discover some novel PARP-1 inhibitors in the near future.

Introduction: The world is currently facing a pandemic initiated by the new coronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus. Viral transcription and replication are the fundamental processes of any virus. They allow the synthesis of genetic material and the consequent multiplication of the virus to infect other cells or organisms. Methods: The most important protein in SARS-CoV-2 is the RNA polymerase (RdRp or nsp12), responsible for both processes. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for a drug search, like virtual screening and molecular docking. Here, the Pathogen Box database of chemical compounds was used together with Remdesivir, Beclabuvir, and Sofosbuvir drugs as potential inhibitors of nsp12. Results: The results showed Top10 potential target inhibitors with binding energy (ΔG) higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with ΔG = −7.53 kcal/mol, present interactions with three important residues of the nsp12 catalytic site. Conclusion: These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be considered as drugs for the development of effective treatments against this new pandemic.

Introduction: A series of hydrophobic phenylacetic acid derivatives introducing an aromatic lipophilic side chain at C-3 amino and an acetyl or isopropionyl at C-4 amino were synthesized and evaluated for their ability to inhibit neuraminidase (NA) of influenza A virus. Methods: All compounds were synthesized in good yields starting from commercially available 2-(4- aminophenyl) acetic acid using a suitable synthetic strategy. Results: These compounds showed potent inhibitory activity against influenza A NA. Several compounds with alkylated amino group showed moderate NA subtype selectivity, among which compound (7i) displayed the best. Conclusion: Compound (7i) activity against H5N1 was more than 10 times better than H9N2, and could be used as lead compounds in the future.

Background: Immune and inflammatory reactions are important factors leading to secondary spinal cord injury. Aims: This study aimed to investigate the effect of BCG on behavior after acute spinal cord injury in rats and its related mechanisms. Methods: Rats with spinal cord injury were generated according to modified Allen’s method. Rats were divided into the BCG group (rats with spinal cord injury intraperitoneally injecting with BCG), Model group (rats with spinal cord injury intraperitoneally injecting with normal saline), and Sham group (normal rats intraperitoneally injecting with normal saline). Basso, Beattie, and Bresnahan (BBB) scoring system was used for evaluating behavioral outcomes. Foxp3 expression in spinal cord tissues was evaluated using immunofluorescence analysis. HE staining was used for assessing the injury of spinal cord tissues. Results: BBB scores of the Model group were remarkably lower compared to that of the Sham group (P<0.05). Foxp3 expression was significantly downregulated in the Model group compared with that of the Sham group (P<0.05). BBB scores of the BCG group were significantly higher compared to that of the Model group at 3, 5, 7, and 14 days post-treatment (P<0.05). In the BCG group, there were fewer inflammatory cells, smaller cavities, and a complete structural arrangement than in the Model group. BCG treatment significantly reduced the spinal cord injury score compared to that of the Model group (P<0.05). Post BCG treatment, Foxp3 expression was predominantly enhanced compared with that of the Model group (P<0.05). Conclusion: BCG could affect inflammation after spinal cord injury through upregulating the expression of Foxp3 and further promote the recovery of hindlimb motor function in rats with spinal cord injury.

Objective: Asiaticoside (AS), an active compound extracted from Centella asiatica, can promote the osteogenic differentiation of human periodontal ligament cells. In this study, we investigated the impact of AS on lipopolysaccharide (LPS)-induced osteoblast differentiation and inflammatory response in human periodontal ligament stem cells (hPDLSCs) and its possible mechanisms. Methods: hPDLSCs were treated with LPS to establish a model mimicking periodontitis and then administered with different concentrations of AS (30, 60, and 120 μM). Flow cytometry and CCK-8 were conducted to assess cell apoptosis and proliferation rates, ELISA to detect the levels of inflammatory factors (IL-1β, IL-8, and TNF-α) in the cell supernatant, and Western blot to determine the expression of osteoblast differentiation proteins (Runx2, and OPN) and TLR4/NF-ΚB signaling pathway proteins (TLR4, MyD88, P65, p-P65) with ALP and Alizarin red staining conducted. Results: LPS induced apoptosis of hPDLSCs, and inhibited proliferation and osteoblast differentiation when increasing the levels of inflammatory factors. However, these alterations were restored upon AS treatment dose-dependently when cell apoptosis decreased, proliferation rate increased, IL-1β, IL-8, TNF- α levels decreased, and osteoblast differentiation enhanced. Additionally, LPS activated the TLR4/NF-ΚB signaling pathway in hPDLSCs, up-regulating TLR4, MyD88, and p-P65 expression, which was abrogated by AS. Conclusion: AS ameliorates LPS-induced inflammation and apoptosis in hPDLSCs through TLR4/NF- ΚB pathway and that AS can be expected to become a therapeutic drug for periodontal tissue regeneration treatment.

Background: Cerebral stroke is one of the leading causes of death and disability in a large number of patients globally. Brain damage in ischemic stroke is led by a complex cascade of events. The Rho-associated kinase-2 (ROCK2) has a significant role in cerebral vasospasm, vascular remodeling, and inflammation. It is activated in cerebral ischemia and its inhibition leads to a neuroprotective effect. Objective: The present study is designed to identify potential inhibitors of ROCK2 using a molecular docking approach. Methods: We docked phytochemicals of Withania somnifera (WS) into the catalytic site of ROCK2 and compared results with inhibitor Y-27632. ADME and drug-likeness properties of WS phytochemicals were also analyzed. Results: Results suggest that 11 phytochemicals exhibited higher binding affinity toward the ROCK2 catalytic domain compared to the Y-27632 inhibitor. Among these phytochemicals, Withanolide G formed H-bonding and established hydrophobic contacts with key catalytic domain residues of ROCK2. Conclusion: Our findings suggest that Withanolide G has the potential to inhibit the action of ROCK2 and can be developed as a neurotherapeutic agent to combat cerebral ischemic insult.

Background: Cancer is a serious threaten to human life, and drug developers are pushing hard to discover potent anticancer agents. Pyrimidine and flavonoids are both attractive entities in medicinal chemistry; it is necessary to get new cancer drugs capitalizing on the two frameworks. Objective: This work includes the synthesis of series chrysin derivatives containing different substituted pyrimidines and an evaluation of their in vitro anticancer activity. Methods: Chrysin was merged with different substituted pyrimidines. Their antiproliferative activity was screened against five cancer cell lines (A549, HepG2, HCT116, MCF-7, and PC-3) using MTS method, and the marketed anticancer drug erlotinib was used as a reference. Results: Seventeen chrysin derivatives were synthesized. Compound 33E showed the best activity against A549, HepG2, MCF-7, and PC-3 cells, with IC50 values of 30.30 μM, 21.02 μM, 24.67 μM, 22.13 μM in A549, HepG2, MCF-7, PC-3 cells, respectively. Compound 33A showed the best activity against HCT116 cells, with an IC50 value of 4.83 μM in HCT116 cell lines. Conclusion: In the present study, a new set of chrysin derivatives containing anilinopyrimidine, piperazine- pyrimidine and piperidine-pyrimidine were prepared. Two compounds (33D, 33E) display higher toxicity than erlotinib toward the five cancerous cell lines (A549, HepG2, HCT116, MCF-7, and PC-3), and one compound (33A) exhibits better inhibitory activity than erlotinib to the HCT116 cells. These results underline the significance of the strategy to merge chrysin with different substituted pyrimidines for obtaining efficient anticancer drugs.

Background: Mutations in Penicillin Binding Protein 2B (PBP2B) lead to resistance against commercial β-lactam antibiotics among some strains of Streptococcus pneumoniae. In this study, the molecular mechanism of resistance and the alternate strategy for controlling the Penicillin Binding Protein 2B (PBP2B) of resistant G54 and the two intermediate-resistant Hungary19A-6 and SP195 strains of Streptococcus pneumoniae are determined using an in silico approach. Methods: In this study, we considered four ligand compounds, namely ZINC59376795, ZINC36922620, ZINC39550705, and ZINC36953975 of the ZINC database, identified through high-throughput screening (HTS) study for the resistant strain (5204-PBP2B). Glide XP docking and molecular dynamic simulation studies were performed on the PBP2B of the three resistant strains chosen for this study. The stability analysis was performed with prime-MM/GBSA, and the binding free energy, RMSD, and RMSF were also evaluated. Results: Out of the four ligands, the ZINC39550705 ligand was found to form a stable complex with PBP2B of all three strains. Furthermore, this ZINC39550705 ligand was observed to form four hydrogen bonds with the PBP2B of all three strains. Molecular dynamics simulations were performed with these four selected ligands and targets. The resulting binding pattern, RMSD, RMSF, and hydrogen bond calculation analyses provide deeper insight into the molecular interactions of these four selected ligands with the PBP2B of the three resistance strains of S. pneumoniae. Conclusion: The interaction of the selected ligand molecules and PBP2B of the resistant strains of S. pneumoniae revealed that hydroxyl amino acid Thr at position 224, acidic amino acids including Glu at positions 301, 245, and 240, amidic amino acids, Asn at positions 265 and 260, and aliphatic amino acid Gly at the 302 position had a crucial role in the formation of hydrogen bonds with most of the selected ligands that contributed to the stability of the complexes. The molecular dynamics simulation further confirmed that the stability of ligand ZINC39550705–PBP2B of all mutant strains was higher compared to other ligand-protein complexes evaluated in the present study. Selected ligand molecules showed significant properties of the inhibitor to be used against the resistant strains of S. pneumoniae, and the ligand ZINC39550705, in particular, is a potential alternative to commercial β-lactam antibiotics.

Objective: This study used network pharmacology and molecular docking technology to explore the molecular mechanism of Panax notoginseng in the treatment of disseminated intravascular coagulation. Methods: The main active components and targets of Panax notoginseng were screened by the TCMSP database, and DIC-related targets were obtained from the GeneCards database. PPI network was constructed by String and Cytoscape, GO gene analysis and KEGG pathway enrichment analysis were performed by DAVID, and molecular docking was performed by AutoDock software. Results: Eight active compounds and 51 potential therapeutic targets of Sanqi were screened. The key targets include VEGF, MAPK3, EGFR, STAT3 and so on. Beta-sitosterol, Stigmasterol, quercetin, DFV, and Diop were identified aspotential candidate ingredients. There are 95 KEGG enrichment pathways. The metabolic pathways involving a large number of genes mainly include the PI3K-Akt signaling pathway, Rap1 signaling pathway, VEGF signaling pathway and TNF signaling pathway. Conclusion: This study revealed the multi-component, multi-target and multi-channel action characteristics of Sanqi in the treatment of DIC and predicted the possible pharmacodynamic substances, key targets and action pathways, which provided a theoretical basis for its new drug development and mechanism of action.

Aim: The aim of this study was to carry out synthesis and characterization of nitrogencontaining heterocyclic derivatives of 1,3-thiazolidine-2,4-diones as dual anti-inflammatory and antioxidant agents and their docking studies. Background: Inflammation is a protective mechanism of our body to reduce injury and infection by microorganisms. The COX-2 enzyme is responsible for the production of prostaglandins (PG1), which are responsible for pain, fever, and a variety of other inflammatory symptoms. Reactive oxygen species (ROS) are important signalling molecules during inflammatory diseases. In an inflammatory state, polymorphonuclear neutrophils (PMNs) produce oxidative stress, which causes inter-endothelium junctions to open and the transfer of inflammatory cells over the endothelial barrier to increase. Tissue damage is caused by these inflammatory cells. Objective: The objective was to club thiazolidinediones with benzimidazole, triazole, and indole to achieve an enhanced anti-inflammatory effect. Methods: In the current report, we have synthesized three new series of indole/ benzimidazole/benzotriazole clubbed with 5-arylidene-2,4-thiazolidinediones. The synthesized compounds were tested for in vivo anti-inflammatory activity using a carrageenan-induced rat paw edema model and in vitro antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing ability of plasma (FRAP) and hydrogen peroxide methods. Results: The results demonstrated that the compound PC-5 exhibited significant anti-inflammatory activity with 61.9% inhibition in comparison to the standard drug diclofenac sodium (71.4% inhibition) after 3h. The compound PC-5 exerted the highest antioxidant activity with an IC50 value of 24.68 μM amongst all synthesized compounds. Acute toxicity was also evaluated for all synthesized compounds, and the results indicated that all evaluated compounds were nontoxic in animals. The replacement of benzotriazole with benzimidazole and indole moieties diminished the anti-inflammatory activity. The hydroxysubstituted arylidene showed higher activity than methoxy, chloro substituted arylidene-2,4- thiazolididiones. Docking studies revealed that the compound PC-5 showed higher inhibition activity against the COX-2 receptor rather than COX-1. The ADME properties were also assessed that showed no violation of Lipinski’s rule and no toxicity. Conclusion: The substituents were found to exert varied activity. The docking studies revealed that the compounds showed lesser binding energy with COX-1 as compared to standard drug diclofenac. Moreover, the binding with COX-2 exhibited more binding energy, thereby proving to have specific COX2 inhibitory activity. All synthesised compounds have shown good antioxidant activity in addition to antiinflammatory activity. PC-5, PC-4, PB-5, PB-4, PA-5, and PA-4 were found to have increased antioxidant activity. Because of the presence of an electron-releasing hydroxyl group, PC-5 has proven to be a highly potent antioxidant agent.

Background: Nitrogen-rich heterocycles have occupied a special place in medicinal chemistry due to their exceptional biological activities. In that, thiazolo azapurines and pyrimido thiazolo azapurines are compounds of interest with their medicinal properties. Objective: The objective is to synthesize novel substituted thiazolo azapurines and pyrimido thiazolo azapurines and evaluate their biological activities. Methods: Herein, we have demonstrated the efficient synthesis of thiazole fused triazolo[4,5-d]pyrimidin- 7-ones starting from the easily accessible feedstock chemical cyano acetamide. The reaction proceeds under mild reaction conditions with diversified substrate scope. Results: Notably, the obtained compounds are further derivatized under various sets of conditions to give the corresponding nitrogen-rich tetracyclic core. All synthesized compounds were tested against four pathogenic microorganisms and some of the compounds were found potent with good inhibition. Conclusion: We have synthesized a diversely substituted nitrogen-rich thiazolo azapurines and pyrimido thiazolo azapurines and evaluated them for their anti-bacterial activity. All synthesized compounds were tested against four pathogenic microorganisms, and some of the compounds were found to be potent with good inhibition.

Introduction: The current study aimed to construct a circNR4A1 loaded exosome (EXO) nano system for the treatment of oral squamous cell carcinoma (OSCC) and elucidate the related regulation mechanism in chemoresistance and tumor biology. Methods: Exosomes were isolated from the HEK293 cells by the ultracentrifugation method. Then, the purified nanoproduction was characterized and identified by transmission electron microscopy, dynamic light scattering, and Western blot. The hydrophobic circNR4A1 was then loaded into exosomes by the coincubation method. The effects of circNR4A1 on chemotherapy and apoptosis were evaluated in three multiresistant OSCC cell lines. Results: The range of size distribution of the exosomes was found to be 40-170 nm. Positive TSG101 and CD63 expressions were observed, and the expression of calnexin was negative. In the cisplatin group, circNR4A1 could sensitize 67% of cell lines, while circNR4A1-EXO could sensitize 100% of cell lines. In the 5FU group, circNR4A1 could only sensitize 33% of cell lines, while circNR4A1-EXO could sensitize 67% of cell lines. circNR4A1-EXO is involved in multiple signaling pathways, which can not only activate K-RAS/ERK and MDR-1 signaling pathways but activate DNMT-1 gene expression simultaneously. Conclusion: circNR4A1-EXO can increase the sensitivity of OSCC to anticancer drugs, which may be due to the regulation of the K-RAS/ERK and p53 signaling pathway.

The current study aimed to investigate the protective effect of resveratrol (RSV) on neurovascular units (NVUs) in rats induced by acute cerebral ischemia. RSV could reduce the damage to I/R rats, and the optimal concentration was 40 mg/kg/d. RSV may improve the permeability of the BBB and the destruction of its ultrastructure by upregulating ZO-1, claudin-5, and occludin to reduce the degree of brain edema after IR. Many structures in the NVUs were also damaged after I/R. RSV was found to have a protective effect on NeuN, GFAP, and LN in the NVUs. With the extension of RSV administration time, the protective effect became more significant. This protective effect may be related to the upregulation of NeuN and LN and the inhibition of the expression of GFAP. RSV could reduce neuronal apoptosis by upregulating XIAP and downregulating Smac and caspase-9. The inhibition of RSV on the increase in glial cells may be related to the inhibition of connexin 43 protein expression. RSV could inhibit the content of inflammatory factors IL-1β, IL-6, and TNF-α in the brain tissue of IR rats. RSV has a protective effect on the NVUs-induced injury, which may be related to the regulation of apoptosis and inflammatory signal pathway.

Objective: The present investigation highlights the formulation and evaluation of nanosuspension- loaded transdermal patches of poorly soluble antilipidemic drug (rosuvastatin). Methods: Dissolution characteristics of drug was improved by preparation of nanosuspension employing precipitation–ultrasonication technique using a different blend of water-soluble film forming polymers such as hydroxyl propyl methyl cellulose (HPMC K4M), Eudragit and were further characterized by fourier transformation infrared spectroscopy (FTIR), Malvern zetasizer and SEM. Propylene glycol and tween 80 were used as stabilizers. Based on the particle size of the formulation, the best one of NS4 was selected and fabricated into the transdermal patch by solvent casting method. The prepared formulations were evaluated for various parameters like drug excipient compatibility, appearance, morphology, thickness, tensile strength, folding endurance, % elongation, % moisture content, % moisture uptake, % drug content, in-vitro drug permeation, and stability studies were performed for the optimized formula according to the ICH Q1A (R2) guideline under 4°C and 25°C RH for three months. Results: Amongst all formulation, P4 transdermal patches were considered the optimized formulation. It has the highest in-vitro drug permeation (86.01±0.05%), thickness (0.86±0.09), weight uniformity (475.0±8.60 mg), folding endurance (279.3±9.39), moisture uptake (7.06±1.75%), moisture content (6.81±2.34 %) and stable formula. Conclusion: Therefore, transdermal patches were considered to be potentially suitable for the sustained release of drugs to improve patient compliance.

Introduction: Angiogenesis is involved in many physiological and pathological conditions including cancer. A number of TRP channels induce angiogenesis, promote cell proliferation or induce apoptosis in several types of human cancers. Therefore, TRP channels may be considered potential pharmacological targets for therapeutic options of disorders caused by insufficient angiogenesis or aberrant vascularization. Aims: This study aimed to comparatively investigate in vitro anti-cancer and in vivo anti-angiogenic effects of TRPC blockers Pyr-3 and SKF-96365. Methods: For anti-cancer effects, four cancer cell lines (MDA-MB-231, A549, PC-3, and HCT-116) were used. In vivo anti-angiogenic effects were investigated by employing in vivo CAM assay of fertilized hen eggs. Results: Pyr-3 affected cell viability in a dose-dependent manner, all concentrations of SKF-96365 significantly reduced cell viability in all cell lines. Pyr-3 and SKF-96365 at concentrations of 2.5 μg/pellet and 50 μg/pellet, respectively inhibited in vivo angiogenesis significantly. Conclusion: The concentration of 2.5 μg/pellet caused no irritation, whereas 50 μg/pellet produced some slight irritation. Apart from their anti-cancer effects, our findings indicate that Pyr-3 and SKF-96365 may be promising anti-angiogenic agents for the treatment of angiogenesis-related disorders.

Background: Radix Wikstroemia indica is a traditional Chinese medicine (TCM) used as antiinflammatory and anti-tumor drug. However, it has serious hepatotoxicity, "Sweat soaking method" processed could effectively decrease its hepatotoxicity. Objective: The objective of this study is to study the effects of Radix Wikstroemia indica on six kinds of cytochrome P450(CYP450) isozymes of rat liver microsomes before and after processing, and to study the mechanism of Radix Wikstroemia indica processed by the "Sweat soaking method" to reduce liver toxicity in rats. Methods: In this study, the effects of Radix Wikstroemia indica and processed Radix Wikstroemia indica on the six main CYP450 isoforms (2E1, 1A2, 2C6, 2D1, 2C11, and 3A1) were investigated in vitro. Using a cocktail probe of CYP450 isoform-specific substrates and their metabolites, we carried out in vitro enzymatic studies in liver microsomal incubation systems via UPLC-MS/MS. Results: The results showed that the established UPLC-MS/MS method was precise and reliable. Compared with the blank group, the activities of six enzymes in the RWI and PRWI groups were higher than those in the blank group. At the same dose, the enzyme activities of CYP2E1, CYP1A2, CYP2C6, CYP2C11, and CYP3A1 increased with the increase in dose, and the enzyme activities of the RWI group were higher than those of the PRWI group. The enzyme activities of CYP2E1 and CYP1A2 in the Radix Wikstroemia indica group were significantly increased compared with the blank group, CYP3A1 in the RWI high-dose group was higher than that in the blank group and PRWI group with statistical differences (p < 0.05 or p < 0.01). Conclusion: The processed Radix Wikstroemia indica could reduce liver injury, and its detoxication mechanism might be related to the decrease in enzyme activity of CYP1A2, CYP2E1 and CYP3A1.