Discovery of novel serine/threonine protein phosphatase 1 inhibitors from traditional Chinese medicine through virtual screening and biological assays

Screening and design of PARP12 inhibitors from traditional Chinese medicine small molecules using computational modeling and simulation

The poly (ADP-ribose) polymerase (PARP) family of enzymes plays a pivotal role in orchestrating a multitude of cellular processes, including DNA repair mechanisms, transcriptional regulation, and modulation of immune responses. Within this family, PARP12 emerges as a noteworthy candidate for targeted cancer therapeutics. Consequently, this investigation endeavors to screen and design potential PARP12 inhibitors derived from traditional Chinese medicinal compounds by employing sophisticated molecular modeling and computational medicinal chemistry approaches. The compound RBN2397 is utilized as a benchmark, and the binding efficacies of the newly identified small molecules are assessed against a spectrum of criteria, encompassing molecular interactions, binding free energy, and extensive post-simulation analyses. The outcomes demonstrated that the identified small molecules, specifically tcm8650 and its derivative XC-1, possess remarkable binding affinities and exhibit reduced binding free energies compared to RBN2397. The molecular docking and interaction profiles of these compounds were also comprehensively scrutinized. Moreover, ADMET profiling meticulously evaluated the pharmacokinetic profiles and physicochemical characteristics of these promising molecules and their projected human physiological impact. These computational studies indicated their potential therapeutic applicability and predicted acceptable safety profile, advocating their further exploration as viable candidates in cancer treatment.

Computer especially AI-assisted drug virtual screening and design in traditional Chinese medicine

BACKGROUND

Traditional Chinese medicine (TCM), as a significant part of the global pharmaceutical science, the abundant molecular compounds it contains is a valuable potential source of designing and screening new drugs. However, due to the un-estimated quantity of the natural molecular compounds and diversity of the related problems drug discovery such as precise screening of molecular compounds or the evaluation of efficacy, physicochemical properties and pharmacokinetics, it is arduous for researchers to design or screen applicable compounds through old methods. With the rapid development of computer technology recently, especially artificial intelligence (AI), its innovation in the field of virtual screening contributes to an increasing efficiency and accuracy in the process of discovering new drugs.

PURPOSE

This study systematically reviewed the application of computational approaches and artificial intelligence in drug virtual filtering and devising of TCM and presented the potential perspective of computer-aided TCM development.

STUDY DESIGN

We made a systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Then screening the most typical articles for our research.

METHODS

The systematic review was performed by following the PRISMA guidelines. The databases PubMed, EMBASE, Web of Science, CNKI were used to search for publications that focused on computer-aided drug virtual screening and design in TCM.

RESULT

Totally, 42 corresponding articles were included in literature reviewing. Aforementioned studies were of great significance to the treatment and cost control of many challenging diseases such as COVID-19, diabetes, Alzheimer's Disease (AD), etc. Computational approaches and AI were widely used in virtual screening in the process of TCM advancing, which include structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS). Besides, computational technologies were also extensively applied in absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction of candidate drugs and new drug design in crucial course of drug discovery.

CONCLUSIONS

The applications of computer and AI play an important role in the drug virtual screening and design in the field of TCM, with huge application prospects.

Progress on COVID-19 Chemotherapeutics Discovery and Novel Technology

COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel highly contagious and pathogenic coronavirus that emerged in late 2019. SARS-CoV-2 spreads primarily through virus-containing droplets and small particles of air pollution, which greatly increases the risk of inhaling these virus particles when people are in close proximity. COVID-19 is spreading across the world, and the COVID-19 pandemic poses a threat to human health and public safety. To date, there are no specific vaccines or effective drugs against SARS-CoV-2. In this review, we focus on the enzyme targets of the virus and host that may be critical for the discovery of chemical compounds and natural products as antiviral drugs, and describe the development of potential antiviral drugs in the preclinical and clinical stages. At the same time, we summarize novel emerging technologies applied to the research on new drug development and the pathological mechanisms of COVID-19.

RIPK3-Mediated Necroptosis in Diabetic Cardiomyopathy Requires CaMKII Activation

Activation of Ca²⁺/calmodulin-dependent protein kinase (CaMKII) has been proved to play a vital role in cardiovascular diseases. Receptor-interaction protein kinase 3- (RIPK3-) mediated necroptosis has crucially participated in cardiac dysfunction. The study is aimed at investigating the effect as well as the mechanism of CaMKII activation and necroptosis on diabetic cardiomyopathy (DCM). Wild-type (WT) and the RIPK3 gene knockout (RIPK3^−/−) mice were intraperitoneally injected with 60 mg/kg/d streptozotocin (STZ) for 5 consecutive days. After 12 w of feeding, 100 μL recombinant adenovirus solution carrying inhibitor 1 of protein phosphatase 1 (I1PP1) gene was injected into the caudal vein of mice. Echocardiography, myocardial injury, CaMKII activity, necroptosis, RIPK1 expression, mixed lineage kinase domain-like protein (MLKL) phosphorylation, and mitochondrial ultrastructure were measured. The results showed that cardiac dysfunction, CaMKII activation, and necroptosis were aggravated in streptozotocin- (STZ-) stimulated mice, as well as in (Lepr) KO/KO (db/db) mice. RIPK3 deficiency alleviated cardiac dysfunction, CaMKII activation, and necroptosis in DCM. Furthermore, I1PP1 overexpression reversed cardiac dysfunction, myocardial injury and necroptosis augment, and CaMKII activity enhancement in WT mice with DCM but not in RIPK3^−/− mice with DCM. The present study demonstrated that CaMKII activation and necroptosis augment in DCM via a RIPK3-dependent manner, which may provide therapeutic strategies for DCM.

Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2E69K

The E69K mutation is one of the most frequent protein tyrosine phosphatase-2 (SHP2) mutations in leukemia, and it can cause the increase in the protein activity. Recent studies have shown that the E69K mutation was fairly sensitive to the allosteric inhibitor of SHP2 (SHP099). However, the molecular mechanism of the allosteric drug SHP099 inhibiting SHP2^E69K remains unclear. Thus, the molecular dynamic simulations and the post-dynamics analyses (RMSF, PCA, DCCM, RIN and the binding free energies) for SHP2^WT, SHP2^WT-SHP099, SHP2^E69K and SHP2^E69K-SHP099 were carried out, respectively. Owing to the strong binding affinity of SHP099 to residues Thr219 and Arg220, the flexibility of linker region (residues Val209-Arg231) was reduced. Moreover, the presence of SHP099 kept the autoinhibition state of the SHP2 protein through enhancing the interactions between the linker region and Q loop in PTP domain, such as Thr219/Val490, Thr219/Asn491, Arg220/Ile488 and Leu254/Asn491. In addition, it was found that the residues (Thr219, Arg220, Leu254 and Asn491) might be the key residues responsible for the conformational changes of protein. Overall, this study may provide an important basis for understanding how the SHP099 effectively inhibited the SHP2^E69K activity at the molecular level.

Identification of novel insect β-N-acetylhexosaminidase OfHex1 inhibitors based on virtual screening, biological evaluation, and molecular dynamics simulation

Chitin can be widely found in the fungal cell wall, nematode eggshells, and the exoskeleton of arthropods; however, it is completely absent from higher plants and mammals. The process of chitin degradation is essential for both growth and maturation of insects. Thus, inhibiting chitin degradation is a promising strategy for the control and management of pests. The chitinolytic β-N-acetyl-D-hexosaminidase OfHex1 of Ostrinia furnacalis (one of the most destructive pests) has been suggested as a potential target for the design of eco-friendly pesticides. This study presents the sequential virtual screening of the ZINC library with 8 million compounds, targeting OfHex1. After confirmation via enzyme inhibition experiments, compound 5 exhibited potential inhibitory activity against OfHex1 with a K_i of 28.9 ± 0.5 μM and significant selectivity (IC₅₀ > 100 μM against HsHexB and hOGA). Molecular dynamics simulations combined with binding free energy and free energy decomposition calculations were conducted to investigate the molecular basis underlying the potency of these inhibitors toward OfHex1. The present work provides useful information for the future rational design of novel and potent OfHex1 inhibitorsCommunicated by Ramaswamy H. Sarma.

Tripolyphosphate crosslinked Triticum aestivum (wheatgrass) functionalized antimicrobial chitosan: Ameliorating effect on physicochemical, mechanical, invitro cytocompatibility and cell migration properties

Polymeric films for various biomedical applications require to be biocompatible and non- toxic. Chemical route of modifications for functionalization of the films for improved properties lead to undesirable effects for biological applications. Hence a natural way to enhancing their properties is by functionalizing them using plant extracts. This report investigates the synthesis of bioactive phytochemical loaded polymer using Triticum aestivum (wheatgrass) extract incorporated in tripolyphosphate crosslinked chitosan. Physical and mechanical properties of the extract functionalized crosslinked chitosan were analyzed and this showed significant changes in thickness, tensile strength and % elongation of the blend. The extract functionalized chitosan was characterized using Fourier transform infrared spectroscopy (FT-IR), Scanning electron microscopy (SEM) and Energy dispersive spectroscopy (EDAX) confirming the interaction between the functional moieties of the extract and polymer. Antimicrobial analysis showed improved activity against Escherichia coli and Staphylococus aureus and Candida albicans. Presence of the extract in crosslinked chitosan enhanced the cytocompatibility in 3T3 cells carried out by MTT assay and showed improved cell migration properties determined by scratch assay.Communicated by Ramaswamy H. Sarma.