Exploring anti-malarial potential of FDA approved drugs: an in silico approach

Unlocking nitrogen compounds' promise against malaria: A comprehensive review

Plasmodium parasites are the primary cause of malaria, leading to high mortality rates, which require clinical attention. Many of the medications used in the treatment have resulted in resistance over time. Artemisinin combination therapy (ACT) has shown significant results for the treatment. However, mutations in the parasite have resulted in resistance, leading to decreased efficiency of the medications that are currently being used. Therefore, there is a critical need to find novel scaffolds that are safe, effective, and of economic advantage. Literature has reported several potent molecules with diverse scaffolds designed, synthesized, and evaluated against different strains of Plasmodium. With this growing list of compounds, it is essential to collect the data in one place to gain a concise overview of the emerging scaffolds in recent years. For this purpose, nitrogen-containing heterocycles such as β-carboline, imidazole, quinazoline, quinoline, thiazole, and thiophene have been highly explored due to their wide biological applications. Besides these, another scaffold, benzodiazepine, which is majorly used as a central nervous system depressant, is emerging as an anti-malarial agent. Hence, this review centers on the latest medication advancements designed to combat malaria, emphasizing special attention to 1,4-benzodiazepines as a novel scaffold for antimalarial drug discovery.

Drug Repurposing: A Leading Strategy for New Threats and Targets

Less than 6% of rare illnesses have an appropriate treatment option. Repurposed medications for new indications are a cost-effective and time-saving strategy that results in excellent success rates, which may significantly lower the risk associated with therapeutic development for rare illnesses. It is becoming a realistic alternative to repurposing "conventional" medications to treat joint and rare diseases considering the significant failure rates, high expenses, and sluggish stride of innovative medication advancement. This is due to delisted compounds, cheaper research fees, and faster development time frames. Repurposed drug competitors have been developed using strategic decisions based on data analysis, interpretation, and investigational approaches, but technical and regulatory restrictions must also be considered. Combining experimental and computational methodologies generates innovative new medicinal applications. It is a one-of-a-kind strategy for repurposing human-safe pharmaceuticals to treat uncommon and difficult-to-treat ailments. It is a very effective method for discovering and creating novel medications. Several pharmaceutical firms have developed novel therapies by repositioning old medications. Repurposing drugs is practical, cost-effective, and speedy and generally involves lower risks when compared to developing a new drug from the beginning.

In Silico Screening and Molecular Dynamics Simulation of Potential Anti-Malarial Agents from Zingiberaceae as Potential Plasmodium falciparum Lactate Dehydrogenase (PfLDH) Enzyme Inhibitors

Malaria continues to be a major public health issue in a number of countries, particularly in tropical regions-the emergence of drug-resistant Plasmodium falciparum encourages new drug discovery research. The key to Plasmodium falciparum survival is energy production up to 100 times greater than other parasites, primarily via the PfLDH. This study targets PfLDH with natural bioactive compounds from the Zingiberaceae family through molecular docking and molecular dynamic studies. Sulcanal, quercetin, shogosulfonic acid C, galanal A and naringenin are the Top 5 compounds with a lower binding energy value than chloroquine, which was used as a control in this study. By binding to NADH and substrate binding site residues, the majority of them are expected to inhibit pyruvate conversion to lactate and NAD+ regeneration. When compared to sulcanal and control drugs, the molecular dynamics (MD) simulation study indicated that quercetin may be the most stable molecule when interacting with PfLDH.

Plants as Sources of Natural and Recombinant Antimalaria Agents

Malaria is one of the severe infectious diseases that has victimized about half a civilization billion people each year worldwide. The application of long-lasting insecticides is the main strategy to control malaria; however, a surge in antimalarial drug development is also taking a leading role to break off the infections. Although, recurring drug resistance can compromise the efficiency of both conventional and novel antimalarial medicines. The eradication of malaria is significantly contingent on discovering novel potent agents that are low cost and easy to administer. In this context, plant metabolites inhibit malaria infection progression and might potentially be utilized as an alternative treatment for malaria, such as artemisinin. Advances in genetic engineering technology, especially the advent of molecular farming, have made plants more versatile in producing protein drugs (PDs) to treat infectious diseases, including malaria. These recent developments in genetic modifications have enabled the production of native pharmaceutically active compounds and the accumulation of diverse heterologous proteins such as human antibodies, booster vaccines, and many PDs to treat infectious diseases and genetic disorders. This review will discuss the pivotal role of a plant-based production system that expresses natural antimalarial agents or host protein drugs to cure malaria infections. The potential of these natural and induced compounds will support modern healthcare systems in treating malaria infections, especially in developing countries to mitigate human fatalities.

NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing

Computational methods accelerate the drug repurposing pipelines that are a quicker and cost-effective alternative to discovering new molecules. However, there is a paucity of web servers to conduct fast, focussed, and customized investigations for identifying new uses of old drugs. We present the NOD web server, which has the mentioned characteristics. NOD uses a sensitive sequence-guided approach to identify close and distant homologs of a protein of interest. NOD then exploits this evolutionary information to suggest potential compounds from the DrugBank database that can be repurposed against the input protein. NOD also allows expansion of the chemical space of the potential candidates through similarity searches. We have validated the performance of NOD against available experimental and/or clinical reports. In 65.6% of the investigated cases in a control study, NOD is able to identify drugs more effectively than the searches made in DrugBank. NOD is freely-available at http://pauling.mbu.iisc.ac.in/NOD/NOD/ .

New sulphonamide pyrolidine carboxamide derivatives: Synthesis, molecular docking, antiplasmodial and antioxidant activities

Carboxamides bearing sulphonamide functionality have been shown to exhibit significant lethal effect on Plasmodium falciparum, the causative agent of human malaria. Here we report the synthesis of thirty-two new drug-like sulphonamide pyrolidine carboxamide derivatives and their antiplasmodial and antioxidant capabilities. In addition, molecular docking was used to check their binding affinities for homology modelled P. falciparum N-myristoyltransferase, a confirmed drug target in the pathogen. Results revealed that sixteen new derivatives killed the parasite at single-digit micromolar concentration (IC₅₀ = 2.40–8.30 μM) and compounds 10b, 10c, 10d, 10j and 10o scavenged DPPH radicals at IC₅₀s (6.48, 8.49, 3.02, 6.44 and 4.32 μg/mL respectively) comparable with 1.06 μg/mL for ascorbic acid. Compound 10o emerged as the most active of the derivatives to bind to the PfNMT with theoretical inhibition constant (K_i = 0.09 μM) comparable to the reference ligand pyrazole-sulphonamide (K_i = 0.01 μM). This study identifies compound 10o, and this series in general, as potential antimalarial candidate with antioxidant activity which requires further attention to optimise activity.

Synthesis, molecular docking, antiplasmodial and antioxidant activities of new sulfonamido-pepetide derivatives

Twenty-three new series of toluene-sulfonamide dipeptide derivatives were synthesized and screened for antiplasmodial and antioxidant potencies. Many of the derivatives were active against Plasmodium falciparum with IC50 ranging from 3.20 - 9.10 μM. The ability of compounds 7h, 7m and 7n (IC50 of 7.53, 7.21 and 6.01 μg/mL respectively) to scavenge DPPH free radicals were comparable to that of ascorbic acid. Additionally, molecular docking disclosed that four compounds exhibited theoretical inhibition constant at submicromolar concentrations (K i = 0.72, 0.75, 0.57, and 0.53 μM respectively) compare to the reference ligand (a pyrazole sulfonamide; K i = 0.01 μM). Overall, some of the derivatives possess antimalarial property as well as the ability to inhibit oxidative stress in malaria pathophysiology; and hence, are good candidates for further antimalarial drug research.

Repurposing drugs against the main protease of SARS-CoV-2: mechanism-based insights supported by available laboratory and clinical data

The ongoing global pandemic of COVID-19 has brought life to almost a standstill with the implementation of lockdowns and social distancing as some of the preventive measures in the absence of any approved specific therapeutic interventions. To combat this crisis, research communities worldwide are falling back on the existing repertoire of approved/investigational drugs to probe into their anti-coronavirus properties. In this report, we describe our unique efforts in identifying potential drugs that could be repurposed against the main protease of SARS-CoV-2 (SARS-CoV-2 M^pro). To achieve this goal, we have primarily exploited the principles of 'neighbourhood behaviour' in the protein 3D (workflow-I) and chemical 2D structural space (workflow-II) coupled with docking simulations and insights into the possible modes of action of the selected candidates from the available literature. This integrative approach culminated in prioritizing 29 potential repurpose-able agents (20 approved drugs and 9 investigational molecules) against SARS-CoV-2 M^pro. Apart from the approved/investigational anti-viral drugs, other notable hits include anti-bacterial, anti-inflammatory, anti-cancer and anti-coagulant drugs. Our analysis suggests that some of these drugs have the potential to simultaneously modulate the functions of viral proteins and the host response system. Interestingly, many of these identified candidates (12 molecules from workflow-I and several molecules, belonging to the chemical classes of alkaloids, tetracyclines, peptidomimetics, from workflow-II) are suggested to possess anti-viral properties, which is supported by laboratory and clinical data. Furthermore, this work opens a new avenue of research to probe into the molecular mechanism of action of many drugs, which are known to demonstrate anti-viral activity but are so far not known to target viral proteases.

Exploring the combination characteristics of lumefantrine, an antimalarial drug and human serum albumin through spectroscopic and molecular docking studies

Binding of lumefantrine (LUM), an antimalarial drug to human serum albumin (HSA), the main carrier protein in human blood circulation was investigated using fluorescence quenching titration, UV-vis absorption and circular dichroism (CD) spectroscopy as well as molecular docking. LUM-induced quenching of the protein (HSA) fluorescence was characterized as static quenching, as revealed by the decrease in the value of the Stern-Volmer quenching constant, K_sv with increasing temperature, thus suggesting LUM-HSA complex formation. This was also confirmed from the UV-vis absorption spectral results. Values of the association constant, K_a for LUM-HSA interaction were found to be within the range, 7.27-5.01 × 10⁴ M^-1 at three different temperatures, i.e. 288 K, 298 K and 308 K, which indicated moderate binding affinity between LUM and HSA. The LUM-HSA complex was stabilized by hydrophobic interactions, H-bonds, as well as van der Waals forces, as predicted from the thermodynamic data (ΔS = +50.34 J mol^-1 K^-1 and ΔH = -12.3 kJ mol^-1) of the binding reaction. Far-UV and near-UV CD spectral results demonstrated smaller changes in both secondary and tertiary structures of HSA upon LUM binding, while three-dimensional fluorescence spectra suggested alterations in the microenvironment around protein fluorophores (Trp and Tyr). LUM binding to HSA offered stability to the protein against thermal stress. Competitive drug displacement results designated Sudlow's Site I, located in subdomain IIA of HSA as the preferred binding site of LUM on HSA, which was well supported by molecular docking analysis.Communicated by Ramaswamy H. Sarma.

Prediction of Lipophilicity of some Quinolone Derivatives by using Quantitative Structure-Activity Relationship

OBJECTIVES

Quantitative structure activity relationship (QSAR) was used to study the partition coefficient of some quinolones and their derivatives.

METHODS

These molecules are broad-spectrum antibiotic pharmaceutics. First, data were divided into two categories of train and test (validation) sets using a random selection method. Second, three approaches, including stepwise selection (STS) (forward), genetic algorithm (GA), and simulated annealing (SA) were used to select the descriptors, to examine the effect feature selection methods. To find the relation between descriptors and partition coefficient, multiple linear regression (MLR), principal component regression (PCR) and partial least squares (PLS) were used.

RESULTS

QSAR study showed that both regression and descriptor selection methods have a vital role in the results. Different statistical metrics showed that the MLR-SA approach with (r2=0.96, q2=0.91, pred_r2=0.95) gives the best outcome.

CONCLUSION

The proposed expression by the MLR-SA approach can be used in the better design of novel quinolones and their derivatives.

Combination mode of antimalarial drug mefloquine and human serum albumin: Insights from spectroscopic and docking approaches

The interaction between mefloquine (MEF), the antimalarial drug, and human serum albumin (HSA), the main carrier protein in blood circulation, was explored using fluorescence, absorption, and circular dichroism spectroscopic techniques. Quenching of HSA fluorescence with MEF was characterized as static quenching and thus confirmed the complex formation between MEF and HSA. Association constant values for MEF-HSA interaction were found to fall within the range of 3.79-5.73 × 10⁴  M^-1 at various temperatures (288, 298, and 308 K), which revealed moderate binding affinity. Hydrogen bonds and hydrophobic interactions were predicted to connect MEF and HSA together in the MEF-HSA complex, as deduced from the thermodynamic data (ΔS = +133.52 J mol^-1 K^-1 and ΔH = +13.09 kJ mol^-1 ) of the binding reaction and molecular docking analysis. Three-dimensional fluorescence spectral analysis pointed out alterations in the microenvironment around aromatic amino acid (tryptophan and tyrosine) residues of HSA consequent to the addition of MEF. Circular dichroic spectra of HSA in the wavelength ranges of 200-250 and 250-300 nm hinted smaller changes in the protein's secondary and tertiary structures, respectively, induced by MEF binding. Noncovalent conjugation of MEF to HSA bettered protein thermostability. Site marker competitive drug displacement results suggested HSA Sudlow's site I as the MEF binding site, which was also supported by molecular docking analysis.

Repurposing Drugs Based on Evolutionary Relationships Between Targets of Approved Drugs and Proteins of Interest

Drug repurposing has garnered much interest as an effective method for drug development among biopharmaceutical companies. The availability of information on complete sequences of genomes and their associated biological data, genotype-phenotype-disease relationships, and properties of small molecules offers opportunities to explore the repurpose-able potential of existing pharmacopoeia. This method gains further importance, especially, in the context of development of drugs against infectious diseases, some of which pose serious complications due to emergence of drug-resistant pathogens. In this article, we describe computational means to achieve potential repurpose-able drug candidates that may be used against infectious diseases by exploring evolutionary relationships between established targets of FDA-approved drugs and proteins of pathogen of interest.

eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database

Background

The structural information on proteins in their ligand-bound conformational state is invaluable for protein function studies and rational drug design. Compared to the number of available sequences, not only is the repertoire of the experimentally determined structures of holo-proteins limited, these structures do not always include pharmacologically relevant compounds at their binding sites. In addition, binding affinity databases provide vast quantities of information on interactions between drug-like molecules and their targets, however, often lacking structural data. On that account, there is a need for computational methods to complement existing repositories by constructing the atomic-level models of drug-protein assemblies that will not be determined experimentally in the near future.

Results

We created eModel-BDB, a database of  200,005 comparative models of drug-bound proteins based on   1,391,403 interaction data obtained from the Binding Database and the PDB library of 31 January 2017. Complex models in eModel-BDB were generated with a collection of the state-of-the-art techniques, including protein meta-threading, template-based structure modeling, refinement and binding site detection, and ligand similarity-based docking. In addition to a rigorous quality control maintained during dataset generation, a subset of weakly homologous models was selected for the retrospective validation against experimental structural data recently deposited to the Protein Data Bank. Validation results indicate that eModel-BDB contains models that are accurate not only at the global protein structure level but also with respect to the atomic details of bound ligands.

Conclusions

Freely available eModel-BDB can be used to support structure-based drug discovery and repositioning, drug target identification, and protein structure determination.