Ginger (Zingiber officinale) phytochemicals-gingerenone-A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches

Studies on photocatalytic mineralization of organic pesticides by bimetallic Cu-Zn nanoparticles derived from Zingiber officinale Roscoe (ginger) using green chemistry approach

Compared to monometallic nanoparticles, bimetallic nanoparticle synthesis and characterization have attracted more attention due to their superior environmental protection properties. In this study, we discuss the preparation and characterization of Cu-Zn bimetallic nanoparticles using Zinger extract, as well as their potential role in photocatalytic degradation of carbendazim, chlorpyrifos, monocrotophos, and cypermethrin. Surface properties were assessed with SEM and TEM, while UV-VIS, XRD, FTIR, and fluorescence spectroscopy were used to characterize the materials. It was observed that higher pH conditions were more conducive to the development of stable Cu-Zn BMNPs with diameters ranging from 60 to 100 nm. UV-VIS spectroscopy showed that the Cu-Zn bimetallic nanoparticles photodegraded 53-95% of the pesticides, monocrotophos, chlorpyrifos, and carbendazim during the 24-72-h incubation period. A number of pesticides may be photocatalytically degraded by primary reactive radicals produced by nanoparticles. We propose that the use of bimetallic nanoparticles could be one alternative strategy for pesticide mineralization.

Antimalarial potential, LC-MS secondary metabolite profiling and computational studies of Zingiber officinale

Malaria is among the top-ranked parasitic diseases that pose a threat to the existence of the human race. This study evaluated the antimalarial effect of the rhizome of Zingiber officinale in infected mice, performed secondary metabolite profiling and detailed computational antimalarial evaluation through molecular docking, molecular dynamics (MD) simulation and density functional theory methods. The antimalarial potential of Z. officinale was performed using the in vivo chemosuppressive model; secondary metabolite profiling was carried out using liquid chromatography-mass spectrometry (LC-MS). Molecular docking was performed with Autodock Vina while the MD simulation was performed with Schrodinger desmond suite for 100 ns and DFT calculations with B3LYP (6-31G) basis set. The extract showed 64% parasitaemia suppression, with a dose-dependent increase in activity up to 200 mg/kg. The chemical profiling of the extract tentatively identified eight phytochemicals. The molecular docking studies with plasmepsin II and Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) identified gingerenone A as the hit molecule, and MMGBSA values corroborate the binding energies obtained. The electronic parameters of gingerenone A revealed its significant antimalarial potential. The antimalarial activity elicited by the extract of Z. officinale and the bioactive chemical constituent supports its usage in ethnomedicine.Communicated by Ramaswamy H. Sarma.

Natural medicine delivery from 3D printed bone substitutes

Unmet medical needs in treating critical-size bone defects have led to the development of numerous innovative bone tissue engineering implants. Although additive manufacturing allows flexible patient-specific treatments by modifying topological properties with various materials, the development of ideal bone implants that aid new tissue regeneration and reduce post-implantation bone disorders has been limited. Natural biomolecules are gaining the attention of the health industry due to their excellent safety profiles, providing equivalent or superior performances when compared to more expensive growth factors and synthetic drugs. Supplementing additive manufacturing with natural biomolecules enables the design of novel multifunctional bone implants that provide controlled biochemical delivery for bone tissue engineering applications. Controlled release of naturally derived biomolecules from a three-dimensional (3D) printed implant may improve implant-host tissue integration, new bone formation, bone healing, and blood vessel growth. The present review introduces us to the current progress and limitations of 3D printed bone implants with drug delivery capabilities, followed by an in-depth discussion on cutting-edge technologies for incorporating natural medicinal compounds embedded within the 3D printed scaffolds or on implant surfaces, highlighting their applications in several pre- and post-implantation bone-related disorders.

Bioactivities and green advanced extraction technologies of ginger oleoresin extracts: A review

Zingiber officinale Roscoe is an excellent source of bioactive compounds, mainly gingerols and shogaols compounds, that associated with various bioactivities including antioxidant, anticancer, anti-inflammatory, antimicrobial, and antibiofilm. Zingiber officinale Roscoe found its application in the food, pharmaceutical, and cosmeceutical industries. The demand for a high quality of ginger oleoresin extracts based on the contents of gingerols and shogaols compounds for a health-benefit has dramatically increased. Various extraction techniques, including the conventional and advanced extraction techniques for gingerols and shogaols have been reported based on the literature data from 2012 to 2022. The present review examines the functional composition and bioactivities of Zingiber officinale Roscoe and the advanced green extraction technologies. Some variations in the quantity and quality of gingerols and shogaols compounds are because of the extraction method employed. This review provides a depth discussion of the various green advanced extraction technologies and the influences of process variables on the performance of the extraction process. Lower temperature with a short exposure time such as ultrasound-assisted and enzyme-assisted extraction, will lead to high quality of extracts with high content of 6-gingerol. High thermal processing, such as microwave-assisted and pressurized liquid extraction, will produce higher 6-shogaol. Meanwhile, supercritical fluid extraction promotes high quality and the safety of extracts by using non-toxic CO2. In addition, challenges and future prospects of the extraction of ginger oleoresin have been identified and discussed. The emerging green extraction methods and technologies show promising results with less energy input and higher quality extracts than conventional extraction methods.

Current Understanding of the Molecular Basis of Spices for the Development of Potential Antimicrobial Medicine

Antimicrobial resistance increases day by day around the world. To overcome this situation new antimicrobial agents are needed. Spices such as clove, ginger, coriander, garlic, and turmeric have the potential to fight resistant microbes. Due to their therapeutic properties, medicinal herbs and spices have been utilized as herbal medicines since antiquity. They are important sources of organic antibacterial substances that are employed in treating infectious disorders caused by pathogens such as bacteria. The main focus of the study is the bioactivity of the active ingredients present in different kinds of naturally available spices. We conducted a thorough search of PubMed, Google Scholar, and Research Gate for this review. We have read many kinds of available literature, and in this paper, we conclude that many different kinds of naturally available spices perform some form of bioactivity. After reading several papers, we found that some spices have good antimicrobial and antifungal properties, which may help in controlling the emerging antimicrobial resistance and improving human health. Spices have many phytochemicals, which show good antimicrobial and antifungal effects. This review of the literature concludes that the natural bioactivate compounds present in spices can be used as a drug to overcome antimicrobial resistance in human beings.

Evaluation of tea (Camellia sinensis L.) phytochemicals as multi-disease modulators, a multidimensional in silico strategy with the combinations of network pharmacology, pharmacophore analysis, statistics and molecular docking

Tea (Camellia sinensis L.) is considered as to be one of the most consumed beverages globally and a reservoir of phytochemicals with immense health benefits. Despite numerous advantages, tea compounds lack a robust multi-disease target study. In this work, we presented a unique in silico approach consisting of molecular docking, multivariate statistics, pharmacophore analysis, and network pharmacology approaches. Eight tea phytochemicals were identified through literature mining, namely gallic acid, catechin, epigallocatechin gallate, epicatechin, epicatechin gallate (ECG), quercetin, kaempferol, and ellagic acid, based on their richness in tea leaves. Further, exploration of databases revealed 30 target proteins related to the pharmacological properties of tea compounds and multiple associated diseases. Molecular docking experiment with eight tea compounds and all 30 proteins revealed that except gallic acid all other seven phytochemicals had potential inhibitory activities against these targets. The docking experiment was validated by comparing the binding affinities (Kcal mol^-1) of the compounds with known drug molecules for the respective proteins. Further, with the aid of the application of statistical tools (principal component analysis and clustering), we identified two major clusters of phytochemicals based on their chemical properties and docking scores (Kcal mol^-1). Pharmacophore analysis of these clusters revealed the functional descriptors of phytochemicals, related to the ligand-protein docking interactions. Tripartite network was constructed based on the docking scores, and it consisted of seven tea phytochemicals (gallic acid was excluded) targeting five proteins and ten associated diseases. Epicatechin gallate (ECG)-hepatocyte growth factor receptor (PDB id 1FYR) complex was found to be highest in docking performance (10 kcal mol^-1). Finally, molecular dynamic simulation showed that ECG-1FYR could make a stable complex in the near-native physiological condition.

Multifaceted Pharmacological Potentials of Curcumin, Genistein, and Tanshinone IIA through Proteomic Approaches: An In-Depth Review

Phytochemicals possess various intriguing pharmacological properties against diverse pathological conditions. Extensive studies are on-going to understand the structural/functional properties of phytochemicals as well as the molecular mechanisms of their therapeutic function against various disease conditions. Phytochemicals such as curcumin (Cur), genistein (Gen), and tanshinone-IIA (Tan IIA) have multifaceted therapeutic potentials and various efforts are in progress to understand the molecular dynamics of their function with different tools and technologies. Cur is an active lipophilic polyphenol with pleiotropic function, and it has been shown to possess various intriguing properties including antioxidant, anti-inflammatory, anti-microbial, anticancer, and anti-genotoxic properties besides others beneficial properties. Similarly, Gen (an isoflavone) exhibits a wide range of vital functions including antioxidant, anti-inflammatory, pro-apoptotic, anti-proliferative, anti-angiogenic activities etc. In addition, Tan IIA, a lipophilic compound, possesses antioxidant, anti-angiogenic, anti-inflammatory, anticancer activities, and so on. Over the last few decades, the field of proteomics has garnered great momentum mainly attributed to the recent advancement in mass spectrometry (MS) techniques. It is envisaged that the proteomics technology has considerably contributed to the biomedical research endeavors lately. Interestingly, they have also been explored as a reliable approach to understand the molecular intricacies related to phytochemical-based therapeutic interventions. The present review provides an overview of the proteomics studies performed to unravel the underlying molecular intricacies of various phytochemicals such as Cur, Gen, and Tan IIA. This in-depth study will help the researchers in better understanding of the pharmacological potential of the phytochemicals at the proteomics level. Certainly, this review will be highly instrumental in catalyzing the translational shift from phytochemical-based biomedical research to clinical practice in the near future.

Compounds in Indonesian Ginger Rhizome Extracts and Their Potential for Anti-Skin Aging Based on Molecular Docking

Skin aging is a condition caused by reactive oxygen species (ROS) and advanced glycation end products (AGEs). Indonesian gingers (Zingiber officinale), which consists of Gajah (GG), Red (MM), and Emprit (EE) ginger, are thought to produce anti-skin aging compounds through enzyme inhibition. The enzymes used in the molecular docking study were collagenase, hyaluronidase, elastase, and tyrosinase. This study aimed to determine the compounds contained in Indonesian ginger rhizome ethanolic extracts using liquid chromatography–mass spectrometry/mass spectrometry to differentiate metabolites contained in the different Indonesian ginger rhizome extracts. A principal component analysis (PCA) and a heat map analysis were used in order to determine which compounds and extracts contained potential anti-skin aging properties based on a molecular docking study. Ascorbic acid was used as a control ligand in the molecular docking study. Ninety-eight compounds were identified in three different ginger rhizomes extracts and were grouped into three separate quadrants. The most potent compound for anti-skin aging in the Indonesian ginger rhizome extracts was octinoxate. Octinoxate showed a high abundance in the EE ginger rhizome extract. Therefore, the EE ginger extract was the Indonesian ginger rhizome extract with the greatest potential for anti-skin aging.

Indigenous Nigeria medicinal herbal remedies: A potential source for therapeutic against rheumatoid arthritis

Rheumatoid arthritis (RA) is a debilitating disease associated with locomotion impairment, and conventional therapeutic drugs are not optimal for managing RA. There is an avalanche of medications used for the management of RA. Still, studies have shown that they are associated with severe side effects, including hepatotoxicity, retinopathy, and cardiotoxicity disorders of the central nervous system (CNS), skin, blood, and infections. Complementary and alternative medicine (CAM) is currently gaining attention as a novel panacea for managing debilitating diseases, such as RA. Nigerian folk herbal remedies are replete with a plethora of curative medicine, albeit unvalidated scientifically but with seemingly miraculous provenance. Studies of the identification of bioactive compounds present in these botanicals using advanced spectral analytical techniques have enhanced our understanding of the role of Nigerian herbal remedies in the treatment and management of RA. Interestingly, experimental studies abound that the bioactive compounds present in the extracts of plant botanicals protected animals from the development of RA in different experimental models and reduced the toxicity associated with conventional therapeutics. Validated mechanisms of RA amelioration in human and animal models include suppression of the expression of NF-κB, IL-1β, TNF-α, IL-6, IL-8, IL-17, IL-23, chemokines, TGF-β, RANKL, RANK, iNOS, arginase, COX-2, VEGFA, VEGFR, NFATC1, and TRAP in the synoviocytes. Decreased ROS, NO, MDA, carbonyl groups, and PGE₂ in the synovial fluid increased the expression of PPARα/γ; antioxidant and anti-inflammatory molecules also improve RA etiology. In this mini-review, we discuss the global burden of RA, the novel role of plant-based botanicals as potential therapeutics against signaling pathways in RA. Also addressed is the possible repurposing/reprofiling of plant botanicals to increase their therapeutic index among RA patients that patronize traditional healers in Nigeria with a global projection.

Molecular recognition and binding of CcrA from Bacteroides fragilis with cefotaxime and ceftazidime by fluorescence spectra and molecular docking

In search of new super-bacterial inhibitor agents, the recognition and binding mechanism of the B1 subclass MβL CcrA from Bacteroides fragilis with cefotaxime (CTX) and ceftazidime (CAZ) were studied using spectroscopy analysis and molecular docking. The results showed that the fluorescence quenching of CcrA induced by CTX and CAZ were all due to the complex formation, which belonged to static quenching and was forced by hydrogen bonds and Van der Waals forces, despite the greater binding ability of CTX with CcrA than CAZ. Upon recognizing CTX or CAZ, the CcrA opened its binding pocket by the microenvironmental and conformational of three loops changing to promote an induced-fit of the freshly introduced antibiotics. In addition, the whole antibiotic molecule ultimately entered the active pocket of CcrA with its original carbonate replaced by the carboxyl oxygen of the hexatomic ring adjacent to the β-lactam ring in CTX or CAZ, forming a new tetrahedral coordination structure at the Zn2 site. Moreover, the difference in steric hindrance and electrostatic effects of the side chain affected the binding ability of the two antibiotics to the CcrA. This work showed the refined procedures of the antibiotics binding to CcrA and might provide useful information hint for the new strategy of developing the novel and innovative super-bacterial antibiotics.

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.

Coadministration of Ginger Extract and Fluconazole Shows a Synergistic Effect in the Treatment of Drug-Resistant Vulvovaginal Candidiasis

BACKGROUND

Azoles are the most common antifungal drugs used in the treatment of vulvovaginal candidiasis (VVC). The frequency of azole-resistant Candida isolates has increased dramatically in the last two decades. Here, we assessed the antifungal activity of a combination of fluconazole (FLZ) and methanolic extract of ginger (Meth-Gin) against drug-resistant vulvovaginal candidiasis (VVC) in a murine model.

METHODS

The in vitro activity of FLZ or a combination of FLZ and Meth-Gin was determined against Candida albicans by the agar well diffusion, macrodilution, time-kill and the biofilm eradication methods. The therapeutic efficacy of the formulations was assessed by analyzing the fungal load, pro-inflammatory cytokines, percent apoptotic cells and the histological changes in the vaginal tissues of the mice. Moreover, the renal toxicity the drug formulation was evaluated by analyzing the levels of the blood urea nitrogen (BUN) and creatinine.

RESULTS

The results of in vitro study demonstrated that FLZ did not show any activity against C. albicans, whereas a combination of FLZ and Meth-Gin demonstrated greater activity as shown by the data of the zone of growth inhibition, MIC and time-kill assay. FLZ or Meth-Gin treatment could not completely cure VVC, whereas a combination of FLZ and Meth-Gin was greatly effective in the treatment of VVC. The vaginal tissue from mice of the infected control group had the highest fungal load of 155370 ± 20617 CFUs. Treatment with FLZ at a dose of 40 mg/kg reduced the fungal load to 120863 ± 10723 CFUs. Interestingly, the mice treated with a combination of FLZ (40 mg/kg) and Meth-Gin (200 mg/kg) had a fungal load of 256 ± 152 CFUs. Besides, FLZ and Meth-Gin combination effectively reduced the pro-inflammatory cytokines (IL-1β, TNF-α and IL-17) and the percentage of apoptotic cells in the vaginal tissues. Likewise, the histological analysis revealed the epithelial necrosis, shedding and ulceration in the vaginal tissue, whereas treatment with FLZ and Meth-Gin combination reversed the histopathological changes in the vaginal epithelium and lamina propria.

CONCLUSION

The findings of the current study suggest that the co-administration of Meth-Gin and FLZ may have a potential therapeutic effect in the treatment of azole-resistant candidiasis.

Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products

The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.

Discovery of Lonafarnib-Like Compounds: Pharmacophore Modeling and Molecular Dynamics Studies

Progeria is a globally noticed rare genetic disorder manifested by premature aging with no effective treatment. Under these circumstances, farnesyltransferase inhibitors (FTIs) are marked as promising drug candidates. Correspondingly, a pharmacophore model was generated exploiting the features of lonafarnib. The selected pharmacophore model was allowed to screen the InterBioScreen natural compound database to retrieve the potential lead candidates. A series of filtering steps were applied to assess the drug-likeness of the compounds. The obtained compounds were advanced to molecular docking employing the CDOCKER module available with Discovery Studio (DS). Subsequently, three compounds (Hits) have displayed a higher dock score and demonstrated key residue interactions with stable molecular dynamics simulation results compared to the reference compound. Taken together, we therefore put forth three identified Hits as FTIs that may further serve as chemical spaces in designing new compounds.

Effects of phytochemicals on cellular signaling: reviewing their recent usage approaches

Most of the previous studies in last three decades report evidence of interactions between the different phytochemicals and the proteins involved in signal transduction pathways using in silico, in vitro, ex vivo, and in vivo analyses. However, extrapolation of these findings for clinical purposes has not been that fruitful. The efficacy of the phytochemicals in vivo studies is limited by parameters such as solubility, metabolic degradation, excretion, etc. Various approaches have now been devised to circumvent these limitations. Recently, chemical modification of the phytochemicals are demonstrated to reduce some of the limitations and improve their efficacy. Similar to traditional medicines several combinatorial phytochemical formulations have shown to be more efficient. Further, phytochemicals have been reported to be even more efficient in the form of nanoparticles. However, systematic evaluation of their efficacy, mode of action in pathway modulation, usage and associated challenges is required to be done. The present review begins with basic understanding of how signaling cascades regulate cellular response and the consequences of their dysregulation further summarizing the developments and problems associated with the dietary phytochemicals and also discuss recent approaches in strengthening these compounds in pharmacological applications. Only context relevant studies have been reviewed. Considering the limitations and scope of the article, authors do not claim inclusion of all the early and recent studies.

Natural Flavones from Morus alba against Methicillin-Resistant Staphylococcus aureus via Targeting the Proton Motive Force and Membrane Permeability

The emergence and rapid spread of methicillin-resistant Staphylococcus aureus (MRSA) critically requires alternative therapeutic options. New antibacterial drugs and strategies are urgently needed to combat MRSA-associated infections. Here, we investigated the antibacterial activity of flavones from Morus alba and the potential mode of action against MRSA. Kuwanon G, kuwanon H, mulberrin, and morusin displayed high efficiency in killing diverse MRSA isolates. On the basis of structure-activity analysis, the cyclohexene-phenyl ketones and isopentenyl groups were critical to increase the membrane permeability and to dissipate the proton motive force. Meanwhile, mechanistic studies further showed that kuwanon G displayed rapid bactericidal activity in vitrowith difficulty in developing drug resistance. Kuwanon G targeted phosphatidylglycerol and cardiolipin in the cytoplasmic membrane through the formation of hydrogen bonds and electrostatic interactions. Additionally, kuwanon G promoted wound healing in a mouse model of MRSA skin infection. In summary, these results indicate that flavones are promising lead compounds to treat MRSA-associated infections through disrupting the proton motive force and membrane permeability.

Bioactive Compounds and Bioactivities of Ginger (Zingiber officinale Roscoe)

Ginger (Zingiber officinale Roscoe) is a common and widely used spice. It is rich in various chemical constituents, including phenolic compounds, terpenes, polysaccharides, lipids, organic acids, and raw fibers. The health benefits of ginger are mainly attributed to its phenolic compounds, such as gingerols and shogaols. Accumulated investigations have demonstrated that ginger possesses multiple biological activities, including antioxidant, anti-inflammatory, antimicrobial, anticancer, neuroprotective, cardiovascular protective, respiratory protective, antiobesity, antidiabetic, antinausea, and antiemetic activities. In this review, we summarize current knowledge about the bioactive compounds and bioactivities of ginger, and the mechanisms of action are also discussed. We hope that this updated review paper will attract more attention to ginger and its further applications, including its potential to be developed into functional foods or nutraceuticals for the prevention and management of chronic diseases.

Discovery of Potential Plant-Derived Peptide Deformylase (PDF) Inhibitors for Multidrug-Resistant Bacteria Using Computational Studies

Bacterial peptide deformylase (PDF) is an attractive target for developing novel inhibitors against several types of multidrug-resistant bacteria. The objective of the current study is to retrieve potential phytochemicals as prospective drugs against Staphylococcus aureus peptide deformylase (SaPDF). The current study focuses on applying ligand-based pharmacophore model (PharmL) and receptor-based pharmacophore (PharmR) approaches. Utilizing 20 known active compounds, pharmL was built and validated using Fischer's randomization, test set method and the decoy set method. PharmR was generated from the knowledge imparted by the Interaction Generation protocol implemented on the Discovery Studio (DS) v4.5 and was validated using the decoy set that was employed for pharmL. The selection of pharmR was performed based upon the selectivity score and further utilizing the Pharmacophore Comparison module available on the DS. Subsequently, the validated pharmacophore models were escalated for Taiwan Indigenous Plants (TIP) database screening and furthermore, a drug-like evaluation was performed. Molecular docking was initiated for the resultant compounds, employing CDOCKER (available on the DS) and GOLD. Eventually, the stability of the final PDF⁻hit complexes was affirmed using molecular dynamics (MD) simulation conducted by GROMACS v5.0.6. The redeemed hits demonstrated a similar binding mode and stable intermolecular interactions with the key residues, as determined by no aberrant behaviour for 50 ns. Taken together, it can be stated that the hits can act as putative scaffolds against SaPDF, with a higher therapeutic value. Furthermore, they can act as fundamental structures for designing new drug candidates.

Discovery of Non-Peptidic Compounds against Chagas Disease Applying Pharmacophore Guided Molecular Modelling Approaches

Chagas disease is one of the primary causes of heart diseases accounting to 50,000 lives annually and is listed as the neglected tropical disease. Because the currently available therapies have greater toxic effects with higher resistance, there is a dire need to develop new drugs to combat the disease. In this pursuit, the 3D QSAR ligand-pharmacophore (pharm 1) and receptor-based pharmacophore (pharm 2) search was initiated to retrieve the candidate compounds from universal natural compounds database. The validated models were allowed to map the universal natural compounds database. The obtained lead candidates were subjected to molecular docking against cysteine protease (PDB code: 1ME3) employing -Cdocker available on the discovery studio. Subsequently, two Hits have satisfied the selection criteria and were escalated to molecular dynamics simulation and binding free energy calculations. These Hits have demonstrated higher dock scores, displayed interactions with the key residues portraying an ideal binding mode complemented by mapping to all the features of pharm 1 and pharm 2. Additionally, they have rendered stable root mean square deviation (RMSD) and potential energy profiles illuminating their potentiality as the prospective antichagastic agents. The study further demonstrates the mechanism of inhibition by tetrad residues compromising of Gly23 and Asn70 holding the ligand at each ends and the residues Gly65 and Gly160 clamping the Hits at the center. The notable feature is that the Hits lie in close proximity with the residues Glu66 and Leu67, accommodating within the S1, S2 and S3 subsites. Considering these findings, the study suggests that the Hits may be regarded as effective therapeutics against Chagas disease.