In silico study on indole derivatives as anti HIV-1 agents: a combined docking, molecular dynamics and 3D-QSAR study

Deciphering Saquinavir-Bovine Serum Albumin Interactions: Spectroscopic and Computational Insights

Bovine serum albumin (BSA) plays a crucial role as a carrier protein in plasma, binding various ligands, including drugs. Understanding the interaction between BSA and saquinavir, an antiretroviral drug, is essential for predicting its pharmacokinetics and pharmacodynamics. We employed spectroscopic approaches, including circular dichroism spectrometry and fluorescence spectroscopy, to investigate the binding of saquinavir to BSA. CD studies revealed conformational changes upon saquinavir mesylate binding, and the complex was stable up to 45°C during thermal denaturation. Saquinavir quenched the intrinsic fluorescence of BSA, indicating static quenching due to complex formation. Additionally, molecular docking simulations were performed to elucidate the favored binding site and interactions. The molecular docking results revealed that Subdomains IIA and IIB, which are proximal to Sudlow Site I, are the principal binding sites for the antiviral drug saquinavir. The ligand-bound pose of BSA also revealed that residue Trp213, which is adjacent to saquinavir, further validated the results of the fluorescence quenching assay, suggesting that residue Trp213 is quenched upon binding with saquinavir. MD simulations allowed us to explore the dynamic behavior of the BSA-saquinavir complex over time. We observed conformational fluctuations, solvent exposure, flexibility of binding pockets, free energy landscape, and binding energy. This study enhances our understanding of drug-protein interactions and contributes to drug development and optimization.

Computational study of SENP1 in cancer by novel natural compounds and ZINC database screening

Introduction: Sentrin-specific protease 1 (SENP1) is a protein whose main function is deSUMOylation. SENP1 inhibits apoptosis, and increases angiogenesis, estrogen and androgen receptor transcription and c-Jun transcription factor, proliferation, growth, cell migration, and invasion of cancer. The in vivo and in vitro studies also demonstrated which natural compounds, especially phytochemicals, minerals, and vitamins, prevent cancer. More than 3,000 plant species have been reported in modern medicine. Natural compounds have many anti-cancerous andanti-turmeric properties such as antioxidative, antiangiogenic, antiproliferative, and pro-apoptotic properties. Methods: In this study, we investigated the interaction of some natural compounds with SENP1 to inhibit its activity. We also screened the ZINC database including natural compounds. Molecular docking was performed, and toxicity of compounds was determined; then, molecular dynamics simulation (MDS) and essential dynamics (ED) were performed on natural compounds with higher free binding energies and minimal side effects. By searching in a large library, virtual screening of the ZINC database was performed using LibDock and CDOCKER, and the final top 20 compounds were allowed for docking against SENP1. According to the docking study, the top three leading molecules were selected and further analyzed by MDS and ED. Results: The results suggest that resveratrol (from the selected compounds) and ZINC33916875 (from the ZINC database) could be more promising SENP1 inhibitory ligands. Discussion: Because these compounds can inhibit SENP1 activity, then they can be novel candidates for cancer treatment. However, wet laboratory experiments are needed to validate their efficacy as SENP1 inhibitors.

In-silico discovery of inhibitors against human papillomavirus E1 protein

High-risk (HR) Human papillomavirus (e.g. HPV16 and HPV18) causes approximately two-thirds of all cervical cancers in women. Although the first and second-generation vaccines confer some protection against individuals, there are no approved drugs to treat HR-HPV infections to-date. The HPV E1 protein is an attractive drug target because the protein is highly conserved across all HPV types and is crucial for the regulation of viral DNA replication. Hence, we used the Random Forest algorithm to construct a Quantitative-Structure Activity Relationship (QSAR) model to predict the potential inhibitors against the HPV E1 protein. Our QSAR classification model achieved an accuracy of 87.5%, area under the receiver operating characteristic curve of 1.00, and F-measure of 0.87 when evaluated using an external test set. We conducted a drug repurposing campaign by deploying the model to screen the Drugbank database. The top three compounds, namely Cinalukast, Lobeglitazone, and Efatutazone were analyzed for their cell membrane permeability, toxicity, and carcinogenicity. Finally, these three compounds were subjected to molecular docking and 200 ns-long Molecular Dynamics (MD) simulations. The predicted binding free energies for the candidates were calculated using the MM-GBSA method. The binding free energies for Cinalukast, Lobeglitazone, and Efatutazone were -37.84 kcal/mol, -25.30 kcal/mol, and -29.89 kcal/mol respectively. Therefore, we propose their chemical scaffolds for future rational design of E1 inhibitors.Communicated by Ramaswamy H. Sarma.

Enantioselective Bioactivity, Toxicity, and Degradation in Vegetables and Soil of Chiral Fungicide Mandipropamid

Mandipropamid (MDP) is a widely used chiral fungicide to control oomycete pathogens with two enantiomers. In this study, the enantioselective bioactivity, toxicity, and degradation of MDP were investigated for the first time. The bioactivity of S-MDP was 118-592 times higher than that of R-MDP and 1.14-1.67 times higher than that of Rac-MDP against six phytopathogens. Molecular docking found that S-MDP formed a strong halogen bond with HIS 693 of cellulose synthase and possessed a lower binding energy, which validated the results of the bioactivity assay. S-MDP showed lower toxicity toward Spirodela polyrhiza, while it exhibited higher toxicity in Danio rerio embryo and larva. S-MDP preferentially degraded in cowpea and pepper, while R-MDP preferentially degraded in soil. There is no significant difference between the two enantiomers in the toxicity of adult D. rerio and in cucumber degradation. Therefore, the development of the S-enantiomer was considered as a better option to exhibit high efficiency, which could reduce the residual risk of the pesticide and ensure environmental safety.

Therapeutic potential of indole derivatives as anti-HIV agents: A mini-review

Acquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), is one of the leading causes of human deaths. The advent of different anti-HIV drugs over different disease progress has made AIDS/HIV from a deadly infection to chronic and manageable disease. However, the development of multidrug-resistant viruses, together with the severe side effects of anti-HIV agents, compromised their efficacy and limited the treatment options. Indoles, the most common frameworks in the bioactive molecules, represent attractive scaffolds for the design and development of novel drugs. Indole derivatives are potential inhibitors of HIV enzymes such as reverse transcriptase, integrase and protease, and some indole-based agents like Delavirdine have already been applied in clinics or under clinical evaluations for the treatment of AIDS/HIV, revealing that indole moiety is a useful template for the development of anti-HIV agents. This review focuses on the recent advancement of indole derivatives including indole alkaloids, hybrids, and dimers with anti-HIV potential, covering articles published between 2010 and 2020. The chemical structures, structure-activity relationship and mechanisms of action are also discussed.

A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma

BACKGROUND

Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32).

AIM

The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL.

METHODOLOGY

Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds.

RESULT

MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies.

CONCLUSION

Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.

BMS Derivatives C7-Linked to β-Cyclodextrin and Hyperbranched Polyglycerol Retain Activity against R5-HIV-1NLAD8 Isolates and Can Be Deemed Potential Microbicides

Amides from indole-3-glyoxylic acid and 4-benzoyl-2-methylpiperazine, which are related to entry inhibitors developed by Bristol-Myers Squibb (BMS), have been synthesized with aliphatic chains located at the C7 position of the indole ring. These spacers contain an azido group suitable for the well-known Cu(I)-catalyzed (3+2)-cycloaddition or an activated triple bond for the nucleophilic addition of thiols under physiological conditions. Reaction with polyols (β-cyclodextrin and hyperbranched polyglycerol) decorated with complementary click partners has afforded polyol-BMS-like conjugates that are not cytotoxic (TZM.bl cells) and retain the activity against R5-HIV-1_NLAD8 isolates. Thus, potential vaginal microbicides based on entry inhibitors, which can be called of 4^th generation, are reported here for the first time.

Enantioselective bioactivity, toxicity, and degradation in different environmental mediums of chiral fungicide epoxiconazole

To clarify the environmental behaviour and bioactivity of epoxiconazole enantiomers, an integrated assessment has been done. The degradation in soil, water, and river-sediments were studied. The toxicity to Chlorella vulgaris and Daphnia magna was also examined. The bioactivity to plant-pathogens and molecular docking to CYP51 were investigated. The obtained results showed that the half-lives of R,S-(+)- and S,R-(-)-epoxiconazole were 38.8 and 21.2 days in Jiangsu soil, 43.2 and 22.7 days in Jiangxi soil, 29.1 and 21.3 days in Jilin soil, 43.5 and 32.7 days in anaerobic Jilin soil, 12.3 and 10.1 days in river sediments, and 33.2 and 9.3 days in river water, respectively. Maximum EF was 0.36 in Yangzi-river water. No enantioselective degradation was found in sterilized conditions. The EC₅₀ to C. vulgaris after 48 h was 27.78 mg L^-1, and 18.93 mg L^-1 for R,S-(+)-, and S,R-(-)-epoxiconazole, respectively. The LC₅₀ to D. magna was 4.16 mg L^-1, and 8.49 mg L^-1 for R,S-(+)-, and S,R-(-)-epoxiconazole, respectively. R,S-(+)-epoxiconazole bioactivity was 1.3-7.25 times higher than S,R-(-)-epoxiconazole. In conclusion, R,S-(+)- has higher bioactivity and higher environmental toxicity. In opposite, S,R-(-)- has lower environmental toxicity and lower bioactivity. R,S-(+)-epoxiconazole use is recommended with lower concentrations, which is appropriate for environment safety.

Medicinal chemistry of indole derivatives: Current to future therapeutic prospectives

Indole is a versatile pharmacophore, a privileged scaffold and an outstanding heterocyclic compound with wide ranges of pharmacological activities due to different mechanisms of action. It is an superlative moiety in drug discovery with the sole property of resembling different structures of the protein. Plenty of research has been taking place in recent years to synthesize and explore the various therapeutic prospectives of this moiety. This review summarizes some of the recent effective chemical synthesis (2014-2018) for indole ring. This review also emphasized on the structure-activity relationship (SAR) to reveal the active pharmacophores of various indole analogues accountable for anticancer, anticonvulsant, antimicrobial, antitubercular, antimalarial, antiviral, antidiabetic and other miscellaneous activities which have been investigated in the last five years. The precise features with motives and framework of each research topic is introduced for helping the medicinal chemists to understand the perspective of the context in a better way. This review will definitely offer the platform for researchers to strategically design diverse novel indole derivatives having different promising pharmacological activities with reduced toxicity and side effects.

Combined pharmacophore modeling, 3D-QSAR, homology modeling and docking studies on CYP11B1 inhibitors

The mitochondrial cytochrome P450 enzymes inhibitor steroid 11β-hydroxylase (CYP11B1) can decrease the production of cortisol. Therefore, these inhibitors have an effect in the treatment of Cushing’s syndrome. A pharmacophore model generated by Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD) was used to align the compounds and perform comparative molecular field analysis (CoMFA) with Q² = 0.658, R² = 0.959. The pharmacophore model contained six hydrophobic regions and one acceptor atom, and electropositive and bulky substituents would be tolerated at the A and B sites, respectively. A three-dimensional quantitative structure-activity relationship (3D-QSAR) study based on the alignment with the atom root mean square (RMS) was applied using comparative molecular field analysis (CoMFA) with Q² = 0.666, R² = 0.978, and comparative molecular similarity indices analysis (CoMSIA) with Q² = 0.721, R² = 0.972. These results proved that all the models have good predictability of the bioactivities of inhibitors. Furthermore, the QSAR models indicated that a hydrogen bond acceptor substituent would be disfavored at the A and B groups, while hydrophobic groups would be favored at the B site. The three-dimensional (3D) model of the CYP11B1 was generated based on the crystal structure of the CYP11B2 (PDB code 4DVQ). In order to probe the ligand-binding modes, Surflex-dock was employed to dock CYP11B1 inhibitory compounds into the active site of the receptor. The docking result showed that the imidazolidine ring of CYP11B1 inhibitors form H bonds with the amino group of residue Arg155 and Arg519, which suggested that an electronegative substituent at these positions could enhance the activities of compounds. All the models generated by GALAHAD QSAR and Docking methods provide guidance about how to design novel and potential drugs for Cushing’s syndrome treatment.

Profiling the interaction mechanism of indole-based derivatives targeting the HIV-1 gp120 receptor

A glycoprotein exposed on a viral surface, human immunodeficiency virus type 1 (HIV-1) gp120 is essential for virus entry into cells as it plays a vital role in seeking out specific cell surface receptors for entry.

A review on recent developments of indole-containing antiviral agents

Indole represents one of the most important privileged scaffolds in drug discovery. Indole derivatives have the unique property of mimicking the structure of peptides and to bind reversibly to enzymes, which provide tremendous opportunities to discover novel drugs with different modes of action. There are seven indole-containing commercial drugs in the Top-200 Best Selling Drugs by US Retail Sales in 2012. There are also an amazing number of approved indole-containing drugs in the market as well as compounds currently going through different clinical phases or registration statuses. This review focused on the recent development of indole derivatives as antiviral agents with the following objectives: 1) To present one of the most comprehensive listings of indole antiviral agents, drugs on market or compounds in clinical trials; 2) To focus on recent developments of indole compounds (including natural products) and their antiviral activities, summarize the structure property, hoping to inspire new and even more creative approaches; 3) To offer perspectives on how indole scaffolds as a privileged structure might be exploited in the future.

Docking-based 3D-QSAR study of pyridyl aminothiazole derivatives as checkpoint kinase 1 inhibitors

Checkpoint kinase 1 (Chk1) is a promising target for the design of novel anticancer agents. In the present work, molecular docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on pyridyl aminothiazole derivatives as Chk1 inhibitors. AutoDock was used to determine the probable binding conformations of all the compounds inside the active site of Chk1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed based on the docking conformations and alignments. The CoMFA model produced statistically significant results with a cross-validated correlation coefficient (q2) of 0.608 and a coefficient of determination (r2) of 0.972. The reliable CoMSIA model with q2 of 0.662 and r2 of 0.970 was obtained from the combination of steric, electrostatic and hydrogen bond acceptor fields. The predictive power of the models were assessed using an external test set of 14 compounds and showed reasonable external predictabilities (r(2)pred) of 0.668 and 0.641 for CoMFA and CoMSIA models, respectively. The models were further evaluated by leave-ten-out cross-validation, bootstrapping and progressive scrambling analyses. The study provides valuable information about the key structural elements that are required in the rational design of potential drug candidates of this class of Chk1 inhibitors.