Explaining the autoinhibition of the SMYD enzyme family: A theoretical study

Synthesis, biological evaluation, and computational investigation of ethyl 2,4,6-trisubstituted-1,4-dihydropyrimidine-5-carboxylates as potential larvicidal agents against Anopheles arabiensis

Malaria is one of the most known vector-borne diseases caused by female Anopheles mosquito bites. According to WHO, about 247 million cases of malaria and 619,000 deaths were estimated worldwide in 2021, of which 95% of the cases and 96% of deaths occurred in the African region. Sadly, about 80% of all malaria deaths were of children under five years old. Despite the availability of different insecticides used to control this disease, the emergence of drug-resistant mosquitoes threatens public health. This, in turn, highlighted the need for new larvicidal agents that are effective at different larval life stages. This study aimed to identify novel larvicidal agents. To this end, a series of ethyl 2,4,6-trisubstituted-1,4-dihydropyrimidine-5-carboxylates 8a-i was synthesized using a three-step chemical synthetic approach via a Biginelli reaction employed as a key step. All title compounds were screened against Anopheles arabiensis to determine their larvicidal activities. Among them, two derivatives, ethyl 2-((4-bromophenyl)amino)-4-(4-fluorophenyl)-6-methyl-1,4-dihydropyrimidine-5-carboxylate 8b and ethyl 2-((4-bromo-2-cyanophenyl)amino)-4-(4-fluorophenyl)-6-methyl-1,4-dihydropyrimidine-5-carboxylate 8f, showed the highest larvicidal activity, with mortality of 94% and 91%, respectively, and emerged as potential larvicidal agents. In addition, computational studies, including molecular docking and molecular dynamics simulations, were carried out to investigate their mechanism of action. The computational results showed that acetylcholinesterase appears to be a plausible molecular target for their larvicidal property.Communicated by Ramaswamy H. Sarma.

The design of TOPK inhibitors using similarity search, molecular docking, and MD simulations

Cancer is still a major cause of death worldwide. Unfortunately, the majority of current anticancer treatments suffer many limitations, mainly emergence of resistance and lack of selectivity which necessitate the search for new therapeutics. The TOPK enzyme emerges as a promising target due to its overexpression in many cancer types while being rarely detected in normal tissues. Therefore, targeting TOPK would affect the malignant activity of cancerous cells while sparing normal ones. Further, its vital role in cell division, particularly in cytokinesis, adds to its safety to normal non-multiplying cells. In this study, a combined ligand and structure-based approach was utilized to identify potential TOPK inhibitors. Previously, we identified TOPK inhibitors using a structure-based approach following the construction of a 3D homology model of the TOPK enzyme. Herein, the most active identified inhibitor (lead) was used as a search query to conduct similarity search against PubChem and ChemBridge databases. Retrieved hits were filtered using drug-like filters, docked into the ATP binding site of the enzyme, and finally, the binding free energies of all docked poses were calculated. Based on the computational scores, eight hits were selected as potential TOPK inhibitors. The predicted ADMET descriptors of the eight selected hits were generally favorable. Further, MD simulations of the top scoring hit were conducted to investigate its binding dynamics compared to the lead compound and OTS964 which agreed with the docking results and propose the selected hits as potential TOPK inhibitors. Yet, biochemical testing is still needed to validate these results.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization and larvicidal studies of ethyl 3-benzoyl-7-(piperidin-1-yl)indolizine-1-carboxylate analogues against Anopheles arabiensis and cheminformatics approaches

According to WHO, in 2021, there was an estimation of 247 million malaria cases from 84 malaria-endemic countries. Globally an estimated count of 2 billion malaria cases and 11.7 million deaths due to malaria were recorded in the past two decades. Further, the emergence of drug-resistant mosquitos threatens mankind. Therefore, the development of newer larvicidal agents is the need of the hour. This research identifies a new series of variably substituted indolizines for their effectiveness in controlling Anopheles arabiensis larvae through larvicidal activity. The series of Ethyl 3-benzoyl-7-(piperidin-1-yl)indolizine-1-carboxylate analogues (4a-j) were synthesized by reacting 4-(piperidin-1-yl)pyridine, phenacyl bromides with ethyl propiolate via 1, 3-dipolar cycloaddition and the green metrics of the process are reported. All the newly synthesized compounds were characterized by spectroscopic techniques such as 1H NMR,13C NMR, FT-IR, and HRMS. The larvicidal effectiveness of the newly synthesized compounds was assessed against Anopheles arabiensis. Among the compounds studied, namely 4c, 4d, 4e, and 4f, displayed the most notable larval mortality rates within the series, reaching 73%, 81%, 76%, and 71% respectively, in contrast with the negative control acetone. In comparison, the standard Temephos exhibited a mortality rate of 99% at the same concentration. Furthermore, computational approaches including molecular docking and molecular dynamics simulations identified the potential targets of the series compounds as the larval Acetylcholinesterase (AChE) enzyme and the Sterol Carrier Protein-2 (SCP-2) protein. However, it is essential for these computational predictions to undergo experimental validation.Communicated by Ramaswamy H. Sarma.

Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques

Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.

Down-regulated Smyd1 participated in the inhibition of myoblast differentiation induced by cigarette smoke extract

The histone methyltransferase Smyd1 is essential for muscle development; however, its role in smoking-induced skeletal muscle atrophy and dysfunction has not been investigated thus far. In this study, Smyd1 was overexpressed or knocked down in C2C12 myoblasts by an adenovirus vector and cultured in differentiation medium containing 5% cigarette smoke extract (CSE) for 4 days. CSE exposure resulted in inhibition of C2C12 cell differentiation and downregulation of Smyd1 expression, whereas Smyd1 overexpression reduced the degree of inhibition of myotube differentiation caused by CSE exposure. CSE exposure activated P2RX7-mediated apoptosis and pyroptosis, caused increased intracellular reactive oxygen species (ROS) levels, and impaired mitochondrial biogenesis and increased protein degradation by downregulating PGC1α, whereas Smyd1 overexpression partially restored the altered protein levels caused by CSE exposure. Smyd1 knockdown alone produced a phenotype similar to CSE exposure, and Smyd1 knockdown during CSE exposure aggravated the degree of inhibition of myotube differentiation and the degree of activation of P2RX7. CSE exposure suppressed H3K4me2 expression, and chromatin immunoprecipitation confirmed the transcriptional regulation of P2rx7 by H3K4me2 modification. Our findings suggest that CSE exposure mediates C2C12 cell apoptosis and pyroptosis through the Smyd1-H3K4me2-P2RX7 axis, and inhibits PGC1α expression to impair mitochondrial biosynthesis and increase protein degradation by inhibiting Smyd1 expression, ultimately leading to abnormal C2C12 myoblasts differentiation and impaired myotube formation.

Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases

A comprehensive understanding of the mechanisms involved in epigenetic changes in gene expression is essential to the clinical management of diseases linked to the SMYD family of lysine methyltransferases. The five known SMYD enzymes catalyze the transfer of donor methyl groups from S-adenosylmethionine (SAM) to specific lysines on histones and non-histone substrates. SMYDs family members have distinct tissue distributions and tissue-specific functions, including regulation of development, cell differentiation, and embryogenesis. Diseases associated with SMYDs include the repressed transcription of SMYD1 genes needed for the formation of ion channels in the heart leading to heart failure, SMYD2 overexpression in esophageal squamous cell carcinoma (ESCC) or p53-related cancers, and poor prognosis associated with SMYD3 overexpression in more than 14 types of cancer including breast cancer, colon cancer, prostate cancer, lung cancer, and pancreatic cancer. Given the importance of epigenetics in various pathologies, the development of epigenetic inhibitors has attracted considerable attention from the pharmaceutical industry. The pharmacologic development of the inhibitors involves the identification of molecules regulating both functional SMYD SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) and MYND (Myeloid-Nervy-DEAF1) domains, a process facilitated by available X-ray structures for SMYD1, SMYD2, and SMYD3. Important leads for potential pharmaceutical agents have been reported for SMYD2 and SMYD3 enzymes, and six epigenetic inhibitors have been developed for drugs used to treat myelodysplastic syndrome (Vidaza, Dacogen), cutaneous T-cell lymphoma (Zoinza, Isrodax), and peripheral T-cell lymphoma (Beleodag, Epidaza). The recently demonstrated reversal of SMYD histone methylation suggests that reversing the epigenetic effects of SMYDs in cancerous tissues may be a desirable target for pharmacological development.

The impact of cycleanine in cancer research: a computational study

Cancer is imposing a global health burden because of the steady increase in new cases. Moreover, current anticancer therapeutics are associated with many drawbacks, mainly the emergence of resistance and the severe adverse effects. Therefore, there is a continuous need for developing new anticancer agents with novel mechanisms of action and lower side effects. Natural products have been a rich source of anticancer medication. Cycleanine, a natural product, was reported to exert an antiproliferative effect on ovarian cancer cells by causing apoptosis through activation of caspases 3/7 and cleavage of poly (ADP-ribose) polymerase to form poly (ADP-ribose) polymerase-1 (PARP1). It is well-established that PARP1 is associated with carcinogenesis, and different PARP1 inhibitors are approved as anticancer drugs. In this study, the cytotoxic activity of cycleanine was computationally investigated to determine whether it is a PARP1 inhibitor or a caspase activator. Molecular docking and molecular dynamics (MD) simulations were utilized for this purpose. The results showed that cycleanine has a good binding affinity to PARP1; moreover, MD simulation showed that it forms a stable complex with the enzyme. Consequently, the results showed that cycleanine is a potential inhibitor of the PARP1 enzyme.

Antitubercular, Cytotoxicity, and Computational Target Validation of Dihydroquinazolinone Derivatives

A series of 2,3-dihydroquinazolin-4(1H)-one derivatives (3a–3m) was screened for in vitro whole-cell antitubercular activity against the tubercular strain H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 3l and 3m with di-substituted aryl moiety (halogens) attached to the 2-position of the scaffold showed a minimum inhibitory concentration (MIC) of 2 µg/mL against the MTB strain H37Rv. Compound 3k with an imidazole ring at the 2-position of the dihydroquinazolin-4(1H)-one also showed significant inhibitory action against both the susceptible strain H37Rv and MDR strains with MIC values of 4 and 16 µg/mL, respectively. The computational results revealed the mycobacterial pyridoxal-5′-phosphate (PLP)-dependent aminotransferase (BioA) enzyme as the potential target for the tested compounds. In vitro, ADMET calculations and cytotoxicity studies against the normal human dermal fibroblast cells indicated the safety and tolerability of the test compounds 3k–3m. Thus, compounds 3k–3m warrant further optimization to develop novel BioA inhibitors for the treatment of drug-sensitive H37Rv and drug-resistant MTB.

1,2,3-Triazolyl-tetrahydropyrimidine Conjugates as Potential Sterol Carrier Protein-2 Inhibitors: Larvicidal Activity against the Malaria Vector Anopheles arabiensis and In Silico Molecular Docking Study

Alteration of insect growth regulators by the action of inhibitors is becoming an attractive strategy to combat disease-transmitting insects. In the present study, we investigated the larvicidal effect of 1,2,3-triazolyl-pyrimidinone derivatives against the larvae of the mosquito Anopheles arabiensis, a vector of malaria. All compounds demonstrated insecticidal activity against mosquito larvae in a dose-dependent fashion. A preliminary study of the structure-activity relationship indicated that the electron-withdrawing substituent in the para position of the 4-phenyl-pyrimidinone moiety enhanced the molecules' potency. A docking study of these derivatives revealed favorable binding affinity for the sterol carrier protein-2 receptor, a protein present in the intestine of the mosquito larvae. Being effective insecticides against the malaria-transmitting Anopheles arabiensis, 1,2,3-triazole-based pyrimidinones represent a starting point to develop novel inhibitors of insect growth regulators.

The design of TOPK inhibitors using structure-based pharmacophore modeling and molecular docking based on an MD-refined homology model

The TOPK enzyme (also known as PBK) is a serine-threonine protein kinase that is rarely detected in normal tissues yet is found to be overexpressed and activated in a variety of cancers such as lung, colorectal, breast, and esophageal cancer. Its prevalence in cancerous cells is associated with their poor prognosis and responsiveness to treatment. This enzyme plays a vital role in cell division, specifically in regulating cytokinesis. Unlike drugs targeting early phases in mitosis, inhibition of cytokinesis by targeting biomolecules that are unique to multiplying cells poses no threat to the normal function of non-multiplying cells. Studies have shown that inhibition of cytokinesis is promising in suppressing the growth of proliferating cancerous cells as exemplified by the complete tumor regression seen with the suppression of TOPK. Herein, we report the identification of potent TOPK inhibitors with anticancer potential using a structure-based drug design approach. The only available crystal structure of TOPK corresponds to a double mutant (T9E and T198E) dimer with a distorted N-lobe conformation, thus 3D homology modeling was implemented to rebuild the enzyme's native conformation. The resulting refined model was used to generate 3D pharmacophore models for the virtual screening of small molecules databases. Retrieved hits were filtered, docked into the ATP binding site of the enzyme, rescored, and the binding free energies for the top consensually scoring hits were calculated. Consequently, 45 compounds were selected and their in vitro inhibitory activity against TOPK was tested revealing four potential hits with the most active compound having an IC₅₀ of 3.85 µM. This compound will be chosen as a lead compound to synthesize analogs aiming to enhance potency and drug-like properties and to enrich the SAR data.

In vitro anti-TB properties, in silico target validation, molecular docking and dynamics studies of substituted 1,2,4-oxadiazole analogues against Mycobacterium tuberculosis

The alarming increase in multi- and extensively drug-resistant (MDR and XDR) strains of Mycobacterium tuberculosis (MTB) has triggered the scientific community to search for novel, effective, and safer therapeutics. To this end, a series of 3,5-disubstituted-1,2,4-oxadiazole derivatives (3a-3i) were tested against H37Rv, MDR and XDR strains of MTB. Of which, compound 3a with para-trifluorophenyl substituted oxadiazole showed excellent activity against the susceptible H37Rv and MDR-MTB strain with a MIC values of 8 and 16 µg/ml, respectively.To understand the mechanism of action of these compounds (3a-3i) and identify their putative drug target, molecular docking and dynamics studies were employed against a panel of 20 mycobacterial enzymes reported to be essential for mycobacterial growth and survival. These computational studies revealed polyketide synthase (Pks13) enzyme as the putative target. Moreover, in silico ADMET predictions showed satisfactory properties for these compounds, collectively, making them, particularly compound 3a, promising leads worthy of further optimisation.

Tackling COVID-19: identification of potential main protease inhibitors via structural analysis, virtual screening, molecular docking and MM-PBSA calculations

The widespread of the COVID-19 disease, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), had severely affected the entire world. Unfortunately, no successful vaccines or antiviral drugs are currently available which leaves the scientific community under huge pressure to tackle this pandemic. Among the identified promising druggable targets, specific to this virus, is the main protease (M^pro) enzyme, which is vital for viral replication, transcription and packaging within the host cells. In this study, selective inhibition of the M^pro was sought via thorough analysis of its available structural data in the Protein Data Bank. To this end, COVID-19 M^pro crystal complexes were explored and the key interacting residues (KIRs) within its active site, that are expected to be vital for effective ligand binding, were identified. Based on these KIRs, 3D pharmacophore models were generated and used in virtual screening of different databases. Retrieved hits were docked into the active site of the enzyme and their MM-PBSA based free binding energies were calculated. Finally, ADMET descriptors were calculated to aid the selection of top scoring hits with best ADMET properties. Nine compounds with different chemotypes were identified as potential M^pro inhibitors. Further, MD simulations of a virtual complex of M^pro with one of the promising hits revealed stable binding which is indicative of good inhibitory potential. The identified compounds in this study are expected to support the global drug discovery efforts in fighting against this highly contagious virus by narrowing the searchable chemical space for potential effective therapeutics.Communicated by Ramaswamy H. Sarma.

SMYD2 promotes cervical cancer growth by stimulating cell proliferation

Background

Cervical cancer is the most common gynecological malignancy with low terminal cure rate, and therefore new therapeutic targets are urgently needed to combat this disease. SMYD2, as an oncogene, is abnormal highly expressed in multiple types of tumors and further affects the occurrence and development, but the potential correlations between SMYD2 expression and cervical cancer progression is still unclear.

Methods

We first used the bioinformatics website to screen the data of cervical cancer in (The Cancer Genome Atlas) TCGA and survival analysis was used to find the different survival rates in the SMYD2 high expression group and low expression group. Through immunohistochemistry, the association between SMYD2 expression and clinical-pathological features of cervical cancer patients was further evaluated. Quantitative PCR and Immunoblot were applied to investigate the relative mRNA and protein expression levels, respectively. In vivo and in vitro experiments were performed to explore the function of SMYD2 in cancer progression.

Results

We first found a high expression of SMYD2 in cervical cancer, and survival analysis found that the poorer survival rate in the SMYD2 high expression group than that in the low expression group. Herein, our study demonstrated that the expression of SMYD2 in patients with cervical cancer was associated with FIGO stage, tumor size and further correlated with poor prognosis. Our data further showed that the inhibition of SMYD2 expression in cervical cancer cell line Caski and Siha could dramatically block the proliferation of cervical cancer cells. Additionally, SMYD2-shRNA lentivirus infected remarkably inhibited tumorigenesis in mice compared with the scramble group.

Conclusions

Taken together, this study provides strong evidence of the involvement of SMYD2 in cervical cancer growth and indicates that it could have high potential as a therapeutic target of cervical cancer.

Expression patterns and the prognostic value of the SMYD family members in human breast carcinoma using integrative bioinformatics analysis

Suppressor of variegation, Enhancer of Zeste, Trithorax and Myeloid-Nervy-DEAF1 domain-containing (SMYD) proteins are a set of lysine methyltransferases involved in a range of diverse biological functions, including gene expression, and regulation of skeletal and cardiac-muscle development. These proteins may additionally serve roles in a number of different types of cancer. However, the roles of the five SMYD proteins, SMYD 1/2/3/4/5, their expression patterns and prognostic value remain unclear. In the present study, the transcriptional expression levels of the five SMYD proteins were compared with the survival data of patients with breast carcinoma (BC) from the ONCOMINE dataset, Breast Cancer Gene-Expression Miner v4.0, Kaplan-Meier Plotter, The Cancer Genome Atlas and cBioPortal. An increase in the SMYD2/3/5 mRNA expression levels and a decrease in SMYD1/4 mRNA expression levels in BC tissues compared with normal tissues were identified. Increased SMYD3 mRNA and decreased SMYD5 mRNA expression levels were associated with decreased levels of histological differentiation, according to the Scarff-Bloom-Richardson grading system. Kaplan-Meier curves demonstrated that the increased SMYD1/4 and decreased SMYD2/3 mRNA expression levels were associated with good relapse-free survival (RFS) in patients with BC. Furthermore, SMYD2 mRNA expression levels were associated with the RFS of patients with BC with metastatic relapse, and SMYD4 may serve as a tumor suppressor in patients with BC, as patients with increased SMYD4 mRNA expression levels had significantly better RFS compared with decreased SMYD4 mRNA expression levels. The present data suggested that SMYD2 and SMYD3 may be potential biomarkers for diagnosis of BC. Additionally, SMYD2 and SMYD4 may be potential prognostic indicators of patients with BC.

The Smyd Family of Methyltransferases: Role in Cardiac and Skeletal Muscle Physiology and Pathology

Protein methylation plays a pivotal role in the regulation of various cellular processes including chromatin remodeling and gene expression. SET and MYND domain-containing proteins (Smyd) are a special class of lysine methyltransferases whose catalytic SET domain is split by an MYND domain. The hallmark feature of this family was thought to be the methylation of histone H3 (on lysine 4). However, several studies suggest that the role of the Smyd family is dynamic, targeting unique histone residues associated with both transcriptional activation and repression. Smyd proteins also methylate several non-histone proteins to regulate various cellular processes. Although we are only beginning to understand their specific molecular functions and role in chromatin remodeling, recent studies have advanced our understanding of this relatively uncharacterized family, highlighting their involvement in development, cell growth and differentiation and during disease in various animal models. This review summarizes our current knowledge of the structure, function and methylation targets of the Smyd family and provides a compilation of data emphasizing their prominent role in cardiac and skeletal muscle physiology and pathology.