Potential repurposing of four FDA approved compounds with antiplasmodial activity identified through proteome scale computational drug discovery and in vitro assay

Discovery of Potent Antimalarial Type II Kinase Inhibitors with Selectivity over Human Kinases

While progress has been made in the effort to eradicate malaria, the disease remains a significant threat to global health. Acquired resistance to frontline treatments is emerging in Africa, urging a need for the development of novel antimalarial agents. Repurposing human kinase inhibitors provides a potential expedited route given the availability of a diverse array of kinase-targeting drugs that are approved or in clinical trials. Phenotypic screening of a library of type II human kinase inhibitors identified compound 1 as a lead antimalarial, which was initially developed to target human ephrin type A receptor 2 (EphA2). Here, we report a structure-activity relationship study and lead optimization of compound 1, which led to compound 33, with improved antimalarial activity and selectivity.

Deep computational phenotyping of genomic variants impacting the SET domain of KMT2C reveal molecular mechanisms for their dysfunction

Introduction: Kleefstra Syndrome type 2 (KLEFS-2) is a genetic, neurodevelopmental disorder characterized by intellectual disability, infantile hypotonia, severe expressive language delay, and characteristic facial appearance, with a spectrum of other distinct clinical manifestations. Pathogenic mutations in the epigenetic modifier type 2 lysine methyltransferase KMT2C have been identified to be causative in KLEFS-2 individuals. Methods: This work reports a translational genomic study that applies a multidimensional computational approach for deep variant phenotyping, combining conventional genomic analyses, advanced protein bioinformatics, computational biophysics, biochemistry, and biostatistics-based modeling. We use standard variant annotation, paralog annotation analyses, molecular mechanics, and molecular dynamics simulations to evaluate damaging scores and provide potential mechanisms underlying KMT2C variant dysfunction. Results: We integrated data derived from the structure and dynamics of KMT2C to classify variants into SV (Structural Variant), DV (Dynamic Variant), SDV (Structural and Dynamic Variant), and VUS (Variant of Uncertain Significance). When compared with controls, these variants show values reflecting alterations in molecular fitness in both structure and dynamics. Discussion: We demonstrate that our 3D models for KMT2C variants suggest distinct mechanisms that lead to their imbalance and are not predictable from sequence alone. Thus, the missense variants studied here cause destabilizing effects on KMT2C function by different biophysical and biochemical mechanisms which we adeptly describe. This new knowledge extends our understanding of how variations in the KMT2C gene cause the dysfunction of its methyltransferase enzyme product, thereby bearing significant biomedical relevance for carriers of KLEFS2-associated genomic mutations.

Caffeic Acid in Spent Coffee Grounds as a Dual Inhibitor for MMP-9 and DPP-4 Enzymes

Type 2 diabetes mellitus and diabetic foot ulcers remain serious worldwide health problems. Caffeic acid is one of the natural products that has been experimentally proven to have diverse pharmacological properties. This study aimed to assess the inhibitory activity of caffeic acid and ethanolic extract of spent coffee grounds targeting DPP-4 and MMP-9 enzymes and evaluate the molecular interactions through 50-ns molecular dynamics simulations. This study also introduced our new version of PyPLIF HIPPOS, PyPLIF HIPPOS 0.2.0, which allowed us to identify protein-ligand interaction fingerprints and interaction hotspots resulting from molecular dynamics simulations. Our findings revealed that caffeic acid inhibited the DPP-4 and MMP-9 activity with an IC50 of 158.19 ± 11.30 µM and 88.99 ± 3.35 µM while ethanolic extract of spent coffee grounds exhibited an IC50 of 227.87 ± 23.80 µg/100 µL and 81.24 ± 6.46 µg/100 µL, respectively. Molecular dynamics simulations showed that caffeic acid interacted in the plausible allosteric sites of DPP-4 and in the active site of MMP-9. PyPLIF HIPPOS 0.2.0 identified amino acid residues interacting more than 10% throughout the simulation, which were Lys463 and Trp62 in the plausible allosteric site of DPP-4 and His226 in the active site of MMP-9.

In vitro and in silico studies of the antiviral activity of polyhydrated fullerenes against influenza A (H1N1) virus

As of today, influenza viruses remain a relevant target for the development of antiviral compounds due to their rapid evolution and acquisition of the resistance to existing drugs. Fullerene derivatives have already shown the ability to successfully interact with viruses, and polyhydrated fullerenes (or fullerenols) are particularly attractive due to their compatibility with biological fluids and low toxicity. Therefore, the goal of this work was to study the effect of two batches of a mixture of polyhydrated fullerenes with a mass ratio of 78.1% C₆₀/C₇₀ and 21.9% C₇₆/C₇₈/C₈₄ on the influenza A (H1N1) virus. It was determined that the mixture of fullerenols, along with the low toxicity, showed high antiviral activity with a decrease in the viral infectious titer up to 4 orders of magnitude. In addition, studied fullerenols did not affect the hemagglutination process and did not show any significant prophylactic activity. With the help of molecular docking and molecular dynamics simulation, the likely target of fullerenols' action was determined-the binding site of the RNA primer of the viral RNA-dependent RNA polymerase. Therefore, we assume that the high antiviral effect of polyhydrated fullerenes on influenza A virus is related to their interaction with the viral RNA polymerase.

Roles of Virtual Screening and Molecular Dynamics Simulations in Discovering and Understanding Antimalarial Drugs

Malaria continues to be a global health threat, with approximately 247 million cases worldwide. Despite therapeutic interventions being available, patient compliance is a problem due to the length of treatment. Moreover, drug-resistant strains have emerged over the years, necessitating urgent identification of novel and more potent treatments. Given that traditional drug discovery often requires a great deal of time and resources, most drug discovery efforts now use computational methods. In silico techniques such as quantitative structure-activity relationship (QSAR), docking, and molecular dynamics (MD) can be used to study protein-ligand interactions and determine the potency and safety profile of a set of candidate compounds to help prioritize those tested using assays and animal models. This paper provides an overview of antimalarial drug discovery and the application of computational methods in identifying candidate inhibitors and elucidating their potential mechanisms of action. We conclude with the continued challenges and future perspectives in the field of antimalarial drug discovery.

Antiviral Activity of Acetylsalicylic Acid against Bunyamwera Virus in Cell Culture

The Bunyavirales order is a large group of RNA viruses that includes important pathogens for humans, animals and plants. With high-throughput screening of clinically tested compounds we have looked for potential inhibitors of the endonuclease domain of a bunyavirus RNA polymerase. From a list of fifteen top candidates, five compounds were selected and their antiviral properties studied with Bunyamwera virus (BUNV), a prototypic bunyavirus widely used for studies about the biology of this group of viruses and to test antivirals. Four compounds (silibinin A, myricetin, L-phenylalanine and p-aminohippuric acid) showed no antiviral activity in BUNV-infected Vero cells. On the contrary, acetylsalicylic acid (ASA) efficiently inhibited BUNV infection with a half maximal inhibitory concentration (IC₅₀) of 2.02 mM. In cell culture supernatants, ASA reduced viral titer up to three logarithmic units. A significant dose-dependent reduction of the expression levels of Gc and N viral proteins was also measured. Immunofluorescence and confocal microscopy showed that ASA protects the Golgi complex from the characteristic BUNV-induced fragmentation in Vero cells. Electron microscopy showed that ASA inhibits the assembly of Golgi-associated BUNV spherules that are the replication organelles of bunyaviruses. As a consequence, the assembly of new viral particles is also significantly reduced. Considering its availability and low cost, the potential usability of ASA to treat bunyavirus infections deserves further investigation.

Synthesis, molecular docking and dynamics studies of pyridazino[4,5-b]quinoxalin-1(2H)-ones as targeting main protease of COVID-19

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a crisis in public health. Because, the 3CLpro, the main protease of SARS-CoV-2, possesses a critical role in coronavirus replication, many efforts have been devoted to developing various inhibitors to prevent the fast spread of COVID-19. In the current work, a number of various pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives bearing thiadiazine and thiadiazole fragments has been prepared via a straightforward and practical strategy involving the reaction of 2-(ethoxycarbonyl)-3-formylquinoxaline 1,4-dioxide with thiocarbohydrazide under reflux conditions. To determine the bioavailability of pyridazino[4,5-b]quinoxalin-1(2H)-one derivatives, Lipinski's rule of five has been carried out. Regarding this rule, none of the synthesized compounds exhibit any deviation from Lipinski's rule of five. Furthermore, molecular docking and molecular dynamics approaches have been implemented to figure out the potential interactions of products with SARS-CoV-2 main protease. The outcomes of molecular docking studies demonstrate that the phenyl and nitrophenyl substituted pyridazino[4,5-b]quinoxalin-1(2H)-one show the lowest binding affinity among the other compounds, indicating a favorable orientation in the active site of the chymotrypsin-like cysteine protease. In addition, the MD simulation performed to evaluate the stability of the protein-ligand complex represents that the average binding energy of the nitrophenyl complex is less than that of the phenyl complex. Therefore, according to the in silico results, the inhibitory effect of the nitrophenyl complex is more significant than the phenyl complex.Communicated by Ramaswamy H. Sarma.

Structure-guided pharmacophore based virtual screening, docking, and molecular dynamics to discover repurposed drugs as novel inhibitors against endoribonuclease Nsp15 of SARS-CoV-2

COVID-19 (Corona Virus Disease of 2019) caused by the novel 'Severe Acute Respiratory Syndrome Coronavirus-2' (SARS-CoV-2) has wreaked havoc on human health and the global economy. As a result, for new medication development, it's critical to investigate possible therapeutic targets against the novel virus. 'Non-structural protein 15' (Nsp15) endonuclease is one of the crucial targets which helps in the replication of virus and virulence in the host immune system. Here, in the current study, we developed the structure-based pharmacophore model based on Nsp15-UMP interactions and virtually screened several databases against the selected model. To validate the screening process, we docked the top hits obtained after secondary filtering (Lipinski's rule of five, ADMET & Topkat) followed by 100 ns molecular dynamics (MD) simulations. Next, to revalidate the MD simulation studies, we have calculated the binding free energy of each complex using the MM-PBSA procedure. The discovered repurposed drugs can aid the rational design of novel inhibitors for Nsp15 of the SARS-CoV-2 enzyme and may be considered for immediate drug development.

In Silico Drug Repurposing Approach: Investigation of Mycobacterium tuberculosis FadD32 Targeted by FDA-Approved Drugs

Background: Despite the enormous efforts made towards combating tuberculosis (TB), the disease remains a major global threat. Hence, new drugs with novel mechanisms against TB are urgently needed. Fatty acid degradation protein D32 (FadD32) has been identified as a promising drug target against TB, the protein is required for the biosynthesis of mycolic acids, hence, essential for the growth and multiplication of the mycobacterium. However, the FadD32 mechanism upon the binding of FDA-approved drugs is not well established. Herein, we applied virtual screening (VS), molecular docking, and molecular dynamic (MD) simulation to identify potential FDA-approved drugs against FadD32. Methodology/Results: VS technique was found promising to identify four FDA-approved drugs (accolate, sorafenib, mefloquine, and loperamide) with higher molecular docking scores, ranging from -8.0 to -10.0 kcal/mol. Post-MD analysis showed that the accolate hit displayed the highest total binding energy of -45.13 kcal/mol. Results also showed that the accolate hit formed more interactions with FadD32 active site residues and all active site residues displayed an increase in total binding contribution. RMSD, RMSF, Rg, and DCCM analysis further supported that the presence of accolate exhibited more structural stability, lower bimolecular flexibility, and more compactness into the FadD32 protein. Conclusions: Our study revealed accolate as the best potential drug against FadD32, hence a prospective anti-TB drug in TB therapy. In addition, we believe that the approach presented in the current study will serve as a cornerstone to identifying new potential inhibitors against a wide range of biological targets.

Binding Mechanism between Acetylcholinesterase and Drugs Pazopanib and Lapatinib: Biochemical and Biophysical Studies

Tyrosine kinase inhibitors (TKIs) are antitumor compounds that prevent the phosphorylation of proteins in a biological environment. However, the multitarget performance of TKIs promotes them as possible candidates for drug repositioning. In this work, interaction and inhibition studies through spectroscopic and computational techniques to evaluate the binding effectiveness of lapatinib and pazopanib TKIs to acetylcholinesterase (AChE) are reported. The results indicated potent inhibition at the μM level. The types of inhibition were identified, with pazopanib acting through non-competitive inhibition and lapatinib through acompetitive inhibition. The fluorescence suppression studies indicate a static mechanism for lapatinib-AChE and pazopanib-AChE systems, with a binding constant in the order of 10⁵ M^-1. The obtained thermodynamic parameters reveal interactions driven by van der Waals forces and hydrogen bonds in the lapatinib-AChE system (ΔH° and ΔS° < 0). In contrast, the pazopanib-AChE system shows positive ΔH° and ΔS°, characteristic of hydrophobic interactions. The Foster resonance energy transfer study supports the fluorescence studies performed. The 3D fluorescence studies suggest changes in the microenvironment of the tryptophan and tyrosine residues of the protein in contact with lapatinib and pazopanib. The results suggest effective inhibition and moderate interaction of the drugs with AChE, making them interesting for conducting more in-depth repositioning studies as AChE inhibitors.

Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach

Staphylococcus aureus infection is a leading cause of mortality and morbidity in community, hospital and live-stock sectors, especially with the widespread emergence of methicillin-resistant S. aureus (MRSA) strains. To identify new drug molecules to treat MRSA patients, we have undertaken to search essential proteins that are indispensable for their survival but non-homologous to human host proteins. The current study utilizes a subtractive genome and proteome approach to screen the possible therapeutic targets against S. aureus USA300. Bacterial essential genes are obtained from the DEG database and are compared to avoid cross-reactivity with human host genes. In silico analysis shows 198 proteins that may be considered as therapeutic candidates. Depending on their sub-cellular localization, proteins are grouped as either vaccine or drug targets or both. Extracellular proteins such as cell division proteins (Q2FZ91, Q2FZ95), penicillin-binding proteins (Q2FZ94, Q2FYI0) of the bacterial cell wall, phosphoglucomutase (Q2FE11) and lipoteichoic acid synthase (Q2FIS2) are considered as vaccine targets, and their epitopes have been mapped. Altogether, 53 drug targets are identified, which have shown similarity with the drug targets available in the DrugBank database. Predicted drug targets belong to the common metabolic pathways of MRSA, such as fatty acid biosynthesis, folate biosynthesis, peptidoglycan biosynthesis, ribosome, etc. Protein-protein interaction analysis emphasizing peptidoglycan biosynthesis reveals the connection between penicillin-binding proteins, mur-family proteins and FemXAB proteins. In this study, staphylococcal FemA protein (P0A0A5) is subjected to structure-based virtual screening for the drug repurposing approach. There are 20 residues missing in the crystal structure of FemA, and 12 of these residues are located at the catalytic site. The missing residues are modelled, and stereochemistry is checked. FDA approved drugs available in the DrugBank database have been used in virtual screening with FemA in search of potential repurposed molecules. This approach provides us with 10 drugs that may be used in the treatment of methicillin-resistant staphylococcal mediated diseases. AutoDock 4.2 is used for in silico screening and shows a comparable inhibition constant (Ki) for all 10 FDA-approved drugs towards FemA. Most of these drugs are used in the treatment of various cancers, migraines and leukaemia. Protein-drug interaction analysis shows that the drugs mostly interact with hydrophobic residues of FemA. Moreover, Tyr328 and Lys383 contribute largely to hydrogen bondings during interactions. All interacting amino acids that bind to the drugs are part of the active site cavity of FemA.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10989-021-10287-9.

Black tea bioactives as inhibitors of multiple targets of SARS-CoV-2 (3CLpro, PLpro and RdRp): a virtual screening and molecular dynamic simulation study

The global pandemic due to the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken more than a million lives. Lack of definitive vaccine/drugs against this highly contagious virus has accelerated exploratory research on novel natural and synthetic inhibitors. Tea is a rich source of bioactives and known to have antiviral properties. In this study, an in silico strategy involving ADMET property screening, receptor-ligand docking and molecular dynamic (MD) simulation was employed to screen potential tea bio-active inhibitors against three selected targets (RdRp, 3CLpro and PLpro) of SARS-CoV-2. Among the 70 tea bioactives screened, theaflavin 3,3'-di-gallate (TF3), Procyanidin B2 and Theaflavin 3-gallate (TF2a) exhibited highest binding affinities towards RdRp, 3CLpro/Mpro and PLpro targets of SARS-CoV-2 with low docking scores of -14.92, -11.68 and -10.90 kcal/mol, respectively. All of them showed a substantial number of hydrogen bonds along with other interactions in and around the active sites. Interestingly, the top bioactives in our study showed higher binding affinities compared with known antiviral drugs. Further, the top protein-ligand complexes showed less conformational changes during binding when subjected to MD simulation for 100 nanoseconds. The MMPBSA results revealed that RdRp-TF3, 3CLpro-Procyanidin B2 and PLpro-TF2a complexes were stable with binding free energies of -93.59 ± 43.97, -139.78 ± 16.51 and -96.88 ± 25.39 kJ/mol, respectively. Our results suggest that theaflavin 3,3'-digallate, Theaflavin 3-gallate and Procyanidin B2 found in black tea have the potential to act as inhibitors for selected targets of SARS-CoV-2 and can be considered as drug candidates in future studies against COVID-19.