Determination of Novel SARS-CoV-2 Inhibitors by Combination of Machine Learning and Molecular Modeling Methods.

Introduction: Within the scope of the project, this study aimed to find novel inhibitors by combining computational methods. In order to design inhibitors, it was aimed to produce molecules similar to the RdRp inhibitor drug Favipiravir by using the deep learning method.

Methods: For this purpose, a Trained Neural Network (TNN) was used to produce 75 molecules similar to Favipiravir by using Simplified Molecular Input Line Entry System (SMILES) representations.

Synthesis and Anticancer Activity of Novel Indole Derivatives as Dual EGFR/SRC Kinase Inhibitors.

Background: Recent studies showed that the cooperation between c-SRC and EGFR is responsible for more aggressive phenotype in diverse tumors, including glioblastomas and carcinomas of the colon, breast, and lung. Studies show that combination of SRC and EGFR inhibitors can induce apoptosis and delay the acquired resistance to chemotherapy. Therefore, such combination may lead to a new therapeutic strategy for the treatment of EGFR-mutant lung cancer.

Investigating the Activity of Indole-2-on Derivative Src Kinase Inhibitors Against Chronic Myeloid Leukemia Cells.

Background: Src family tyrosine kinases play a potential role in Bcr-Abl-induced leukemogenesis. Src kinase inhibitors are reported as selective inhibitors of chronic myeloid leukemia.

Objective: Since Src kinase inhibitors have an inhibitive effect on chronic myeloid leukemia, indole derivatives (C-1, C-2, C-3) previously found as potent inhibitors of Src kinase were tested against chronic myeloid leukemia in this study.

SAHAquines, Novel Hybrids Based on SAHA and Primaquine Motifs, as Potential Cytostatic and Antiplasmodial Agents.

We report the synthesis of SAHAquines and related primaquine (PQ) derivatives. SAHAquines are novel hybrid compounds that combine moieties of suberoylanilide hydroxamic acid (SAHA), an anticancer agent with weak antiplasmodial activity, and PQ, an antimalarial drug with low antiproliferative activity. The preparation of SAHAquines is simple, cheap, and high yielding.

Drug Repurposing in the Development of Anticancer Agents.

Background: Research into repositioning known drugs to treat cancer other than the originally intended disease continues to grow and develop, encouraged in part, by several recent success stories. Many of the studies in this article are geared towards repurposing generic drugs because additional clinical trials are relatively easy to perform and the drug safety profiles have previously been established.

Objective: This review provides an overview of anticancer drug development strategies which is one of the important areas of drug restructuring.

Overview on Anticancer Drug Design and Development.

Background: Many impediments of current anti-cancer therapies have urged scientists to discover new agents. As a result of growing spectrums of new targets and strategies and recent biological and biotechnological progresses, many anti-cancer agents such as monoclonal antibodies, small molecule tyrosine kinase inhibitors and epigenetic drugs have been reached to clinical trials.

Objectives: This review helps to understand the rationale for the development of inhibitors against major targets such as cell growth, proliferation, survival, angiogenesis and recent targets such as proteasome, heat shock proteins, and epigenetics.

The Effects of 1,3,5-trisubstituted Indole Derivatives on Cell Growth, Apoptosis and MMP-2/9 mRNA Expression of MCF-7 Human Breast Cancer Cells.

Background: Matrix metalloproteinases are known as extracellular matrix degrading enzymes and have important role on tumor progression.

Objective: This study reports the effects of 1,3,5-trisubstituted indole derivatives on cytotoxicity, apoptosis and MMP- 2/MMP-9 mRNA expression of MCF-7 human breast carcinoma cells.

Method: The cytotoxic effects of the compounds on MCF-7 cells were performed by MTT test, and cell proliferation was determined via BrdU incorporation.

Design Strategies, Structures and Molecular Interactions of Small Molecule Src Inhibitors.

In recent years, several small molecules approved by FDA for clinical studies are promising anti-cancer agent. Among the kinases, Abelson Leukaemia (Abl), sarcoma (Src), epidermal growth factor receptor (EGFR) and vascular endotelhial growth factor receptor (VEGFR) are considered as primary molecular targets for selective inhibition and the best successful targeted therapy of tyrosine kinase inhibitors (TKIs) has been achieved in the treatment of Bcr (break point cluster)-Abl leukemia. The majority of type 1 kinase inhibitors target the active conformation of ATP binding site.

Synthesis, Biological, and Computational Evaluation of Novel 1,3,5-Substituted Indolin-2-one Derivatives as Inhibitors of Src Tyrosine Kinase.

Several substituted indolin-2-one derivatives were synthesized and evaluated for their activities against Src kinase. Several compounds showed activity against Src, with IC50 values in the low micromolar range. Among them, compound 2f showed the most significant activity with an IC50 value of 1.

N-substituted Indole-2 and 3-carboxamide derivatives as inhibitors of human protein kinase CK2: in vitro assay and molecular modelling study.

Protein kinase CK2 (Casein Kinase 2) is involved in cell growth; proliferation and suppression of apoptosis. Hence, it strongly promotes cell survival and can be considered an important target for human cancers. In the present study, a series of N-substituted indole-2- and 3-carboxamide derivatives were tested for inhibitions of human recombinant protein kinase CK2 to evaluate their anticancer properties.

Recent development of new substituted indole and azaindole derivatives as anti-HIV agents.

Human immunodeficiency virus-1 (HIV-1) infections cause global health problems. Indole derivatives have been considered as one of the promising HIV inhibitors. Recent inventions have focused on substituted indole and azaindole derivatives that possess unique antiviral activities against HIV-1.

Synthesis, biological evaluation and docking studies of new pyrrolo[2,3-d] pyrimidine derivatives as Src family-selective tyrosine kinase inhibitors.

In this study, the synthesis and potential enzyme interactions of new Pyrrolo[2,3-d]pyrimidine derivatives along with their inhibitory activity against SFK enzymes such as Fyn, Lyn, Hck, and c-Src were reported. The results indicated that compounds were slightly active of tested SFK enzymes in comparison with PP2 for Fyn, A-419259 for Lyn and CGP77675 for c-Src. Compound N-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)-4-(3,4-dimethoxyphenyl)butanamide (5) was identified as a non-selective slight inhibitor against Fyn, Lyn and c-Src.

Synthesis of new indole-2-carboxamide and 3-acetamide derivatives and evaluation their antioxidant properties.

In recent years, antioxidant compounds play an important role as a health-protecting factor. Antioxidants protect cells against the damaging effects of reactive oxygen species (ROS). An imbalance between antioxidants and ROS results in oxidative stress, which leads to cellular damage and it is linked to many vital diseases.

Evaluation of novel aminomethyl indole derivatives as Src kinase inhibitors and antioxidant agents.

Background: Oxidative stress has been implicated in aging and in a variety of diseases affecting the nervous, respiratory, cardiovascular and gastrointestinal system in humans. Reactive oxygen species (ROS) have been associated with mechanisms to activate kinases, such as protein tyrosine kinases, which may initiate malignant transformation. Significant evidences of the activation of protein kinases by oxidative stress brought increased attention to the role of antioxidants in these mechanisms.

Autodisplay of catalytically active human hyaluronidase hPH-20 and testing of enzyme inhibitors.

Hyaluronic acid (HA) is the major biopolymer of the extracellular matrix and contributes significantly to cell proliferation and migration. Human hyaluronidase hPH-20 has been identified as a tumor marker for breast and laryngeal cancer. A hPH-20-autotransporter fusion protein for cell surface display was transformed into Escherichia coli BL21 (DE3) and hPH-20 was displayed on the surface of E.

Investigation of aminomethyl indole derivatives as hyaluronidase inhibitors.

Hyaluronidase inhibitors are of potential therapeutic value for the treatment of a variety of diseases, such as cancer, arthrosis, or bacterial infections. Potent and selective hyaluronidase inhibitors are not known so far, and current approaches to the development of hyaluronidase inhibitors are limited. Elevated levels of hyaluronan (HA) are connected with most malignant tumours.

N-substituted indole-3-imine derivatives and their amine congeners: antioxidant and Src kinase inhibitory effects.

Current evidences demonstrated that the activity of protein kinases can be controlled through oxidative stress induced by reactive oxygen species (ROS) and normalized by antioxidants. Recent studies with ROS, generated by mitochondria, suggested the potential signalling role of these species, where ROS, especially hydrogen peroxide, were proposed as membrane-related signalling components. The protein regulation by cellular redox states has shown that protein tyrosine kinase members, such as Src kinase and some of the members of the Src family kinases (SFKs), are proteins regulated by the cellular oxidation and reduction status.

The role of fluorine substitution in biphenyl methylene imidazole-type CYP17 inhibitors for the treatment of prostate carcinoma.

It has been established that the growth of most prostate carcinomas depends on androgen stimulation. The inhibition of cytochrome P450-17 (CYP17) to block androgen biosynthesis is therefore regarded as a promising approach to therapy. Based on our previously identified lead compound Ref 1, a series of fluorine-substituted biphenyl methylene imidazoles were designed, synthesized, and evaluated as CYP17 inhibitors to elucidate the influence of fluorine on in vitro and in vivo activity.

Evaluation of new indole and bromoindole derivatives as pp60(c-Src) tyrosine kinase inhibitors.

A series of N-benzyl-indole-3-imine-, amine derivatives and their 5-bromo congeners were synthesized and their biological activity were evaluated against the pp60(c-Src) tyrosine kinase target. To afford the imine derivatives, aldehydes were reacted with substituted benzylamines and the corresponding amine derivatives were obtained by NaBH(4) reduction of these imines. Except insoluble N-benzyl-indole-3-imine derivatives, all the derivatives showed some activity against the kinase target.

A study of 3-substituted benzylidene-1,3-dihydro-indoline derivatives as antimicrobial and antiviral agents.

3-Substituted benzylidene-1,3-dihydro-indoline derivatives were tested for their in vitro antibacterial activity against the Gram-negative bacteria Klebsiella pneumoniae, Pseudomonas aeruginosa, Escherichia coli, and the Gram-positive bacteria Bacillus subtilis, Staphylococcus aureus, and for their their in vitro antifungal activity against Candida krusei and Candida albicans. The minimum inhibitory concentration (MIC) values were determined by the 2-fold serial dilution technique in Mueller Hinton broth and Sabouraud dextrose agar using antibacterial and antifungal assays, respectively. For comparison of the antimicrobial activity, rifampicin, ampicillin trihydrate, gentamicin sulfate, and ofloxacin were used as reference antibacterial agents, and fluconazole and amphotericin B were employed as reference antifungal agents.

Synthesis and pp60c-Src tyrosine kinase inhibitory activities of novel indole-3-imine and amine derivatives substituted at N1 and C5.

A series of novel 1,3,5-trisubstituted indole derivatives, namely, N-benzyl 5-phenyl indole-3-imine, N-benzyl-5-(p-fluorophenyl)indole-3-imine and their corresponding amine congeners, were designed and synthesized as pp60(c-Src) tyrosine kinase inhibitors, and their inhibitory activities toward pp60(c-Src) tyrosine kinase were evaluated by in-vitro kinase assay. Pre-screening at two doses of compounds against kinase target revealed that, except for the N-benzyl-5-phenyl indole imine derivatives 7a-7d, all indole derivatives show the target inhibition at varying levels. Consequently, the compounds, 8c, 8f, 8g, and 8h, were selected for prescreening tests.

Novel aminomethylindole derivatives as inhibitors of pp60c-Src tyrosine kinase: synthesis and biological activity.

The pp60(c-Src) is one of the ubiquitously expressed Src family kinases and has important functions in malignant cells, including regulation of cell division, growth factor signaling, and movement. Therefore, investigating new small molecule inhibitors of pp60(c-Src) is important to discover and develop novel therapeutics for cancer and metastasis. Moreover, some of the small molecule inhibitors that do not qualify for therapeutic use may become very useful tool to explore the role of Src kinase in normal cells as well as in a variety of disease models.

Synthesis, biological evaluation, and molecular modeling studies of methylene imidazole substituted biaryls as inhibitors of human 17alpha-hydroxylase-17,20-lyase (CYP17)--part II: Core rigidification and influence of substituents at the methylene bridge.

Thirty-five novel substituted imidazolyl methylene biphenyls have been synthesized as CYP17 inhibitors for the potential treatment of prostate cancer. Their activities have been tested with recombinant human CYP17 expressed in Escherichia coli. Promising compounds were tested for selectivity against CYP11B1, CYP11B2, and hepatic CYP enzymes 3A4, 1A2, 2B6 and 2D6.

Synthesis and evaluation of N-substituted indole-3-carboxamide derivatives as inhibitors of lipid peroxidation and superoxide anion formation.

The in vitro antioxidant effects of novel N-substituted indole-3-carboxamides (I3CDs) 1-10 on rat liver microsomal NADPH-dependent lipid peroxidation (LP) levels and their free radicals scavenging properties were determined by the inhibition of superoxide anion formation (SOD). Among the synthesized compounds, 4, 5, 8 and 9 significantly inhibited SOD with an inhibition range at 84-100% at 10(-3) M concentration. The presence of halo substituents both ortho- and para- positions of these compounds resulted 100% inhibition of SOD.