Current Drug Discovery Technologies - Volume 18, Issue 4, 2021

Background: Machine learning is an active area of research in computer science by the availability of big data collection of all sorts prompting interest in the development of novel tools for data mining. Machine learning methods have wide applications in computer-aided drug discovery methods. Most incredible approaches to machine learning are used in drug designing, which further aid the process of biological modelling in drug discovery. Mainly, two main categories are present which are Ligand-Based Virtual Screening (LBVS) and Structure-Based Virtual Screening (SBVS), however, the machine learning approaches fall mostly in the category of LBVS. Objectives: This study exposits the major machine learning approaches being used in LBVS. Moreover, we have introduced a protocol named FP-CADD which depicts a 4-steps rule of thumb for drug discovery, the four protocols of computer-aided drug discovery (FP-CADD). Various important aspects along with SWOT analysis of FP-CADD are also discussed in this article. Conclusion: By this thorough study, we have observed that in LBVS algorithms, Support Vector Machines (SVM) and Random Forest (RF) are those which are widely used due to high accuracy and efficiency. These virtual screening approaches have the potential to revolutionize the drug designing field. Also, we believe that the process flow presented in this study, named FP-CADD, can streamline the whole process of computer-aided drug discovery. By adopting this rule, the studies related to drug discovery can be made homogeneous and this protocol can also be considered as an evaluation criterion in the peer-review process of research articles.

Schistosome infection is regarded as one of the most important and neglected tropical diseases associated with poor sanitation. Like other living organisms, schistosomes employ multiple biological processes, of which some are regulated by a post-translational modification called Adenosine Diphosphate-ribosylation (ADP-ribosylation), catalyzed by ADP-ribosyltransferases. ADP-ribosylation is the addition of ADP-ribose moieties from Nicotinamide Adenine Dinucleotide (NAD+) to various targets, which include proteins and nucleotides. It is crucial in biological processes such as DNA repair, apoptosis, carbohydrate metabolism and catabolism. In the absence of a vaccine against schistosomiasis, this becomes a promising pathway in the identification of drug targets against various forms of this infection. The tegument of the worm is an encouraging immunogenic target for anti-schistosomal vaccine development. Vaccinology, molecular modeling and target-based drug discovery strategies have been used for years in drug discovery and for vaccine development. In this paper, we outline ADP-ribosylation and other different approaches to drug discovery and vaccine development against schistosomiasis.

Bunium persicum is one of the most medically and economically important species of the Apiaceae family. Despite a variety of phytochemical and experimental research on this species, there is no considerable update on all related outcomes. Accordingly, current work compiles an overview of Cumin’s phytochemical and pharmacological activities. Papers related to phytochemistry, pharmacology and clinical properties of B. persicum were filtered from databases as PubMed, ScienceDirect and Scopus with the term "Bunium persicum" till 15th May 2020. Genetic, pure pharmaceutical and agriculture papers were excluded. Moreover, traditional applications of this herb in Persian medicine were studied and included. In all, 54 papers reporting the compositions, Anticonvulsant, antinociceptive, anti-inflammatory, antioxidant, anti-glycation, antidiarrhea, anti-hematotoxic, anti-toxoplasmosis, hypoglycemic, larvicidal, scolicidal, anticholinergic and antihistaminic activities of B. persicum as well as reducing and stabilizing effects in nanoparticles. Three clinical trials have also been conducted on B. persicum. There are also numerous effects, cited in traditional manuscripts such as gastroprotective, kidney tonic, slimming activity and antidote for poisons. The most dominant chemical composition of Cumin is the essential oil, responsible for various potent antimicrobial and antifungal activities. The herb also contains phenolic and flavonoid compounds that reflect the antioxidant and anti-inflammatory activities. Many of the experimental and pharmacological studies on B. persicum have traces in traditional manuscripts. There are also medical aspects that have not yet been evaluated. Despite various experimental investigations, lack of extensive clinical studies, which is currently limited to few trials on remarked activities of B. persicum is still remained to be covered.

Introduction: Histamine, a biological amine, is considered as a principal mediator of many pathological processes regulating several essential events in allergies and autoimmune diseases. Numerous derivatives have been developed that strive with histamine at the H1 receptor and prevent binding of histamine at the H1 receptor, thereby preventing allergic reactions. Molecules containing a triazole ring fused with six-membered ring systems are found to possess broad applications in the field of medicine and industry. The present study is an attempt to characterize the impact of the nature of the substituent introduced at 5 positions of the-4H-1,2,4-triazole-3-thiol on their capacities to bind with the H1 receptor. Methods: Molecular docking (PDB ID: 3RZE) revealed that synthesized derivatives and target proteins were actively involved in binding with Tyr-108, Thr-112, Ala-216, and Phe-432 subunits. A pharmacophore model, new 5-(4-substituted phenyl)-4-(phenylamino)-4-H-1,2,4-triazole-3- thiols (5a-5h) were designed and evaluated for H1-blocking activity using isolated segments from the guinea pig ileum. Results: According to in silico analysis, all the compounds have a topological polar surface area (TPSA) less than 140 Å squared, so they tend to easily penetrate cell membranes. The results show that most of the compounds are non-inhibitors of CYP450 substrates that play a fundamental role in drug metabolism. Compounds 5d (50.53±12.03), 5h (50.62±12.33) and 7a (55.07±12.41) are more active than others. Conclusion: Finally, these derivatives were screened for H1 receptor antagonist activity using guinea pig ileum, taking chlorpheniramine maleate as a standard. Most of the compounds were found to possess better antihistamine activity.

Background: The only remedy for up surging problem of antibiotic resistance is the discovery of antibacterial agents of natural origin. Objective: The present study was aimed at finding antibacterial potential of crude and solvent extracts of mature leaves of Plumeria pudica. Methods: Antibacterial activity of three different solvent extracts were evaluated in four human and four fish pathogenic bacteria by measuring the zone of inhibition and determining Minimum Inhibitory Concentration and Minimum Bactericidal Concentration values. Standard antibiotics were used as positive control. Preliminary phytochemical screening of most effective extract i.e., ethyl acetate extract, Fourier Transform Infra Red analysis and GC-MS analysis of the Thin Layer Chromatographic (TLC) fraction of ethyl acetate extract were done meticulously. All experiments were done thrice and analyzed statistically. Results: Crude leaf extracts and solvent extracts caused good inhibition of bacterial growth in all selected bacteria. Ethyl acetate extract showed highest inhibition zones in all tested strains with maximum inhibition (19.50±0.29 mm) in Escherichia coli (MTCC 739). MBC/MIC of the extracts indicated that all three solvent extracts were bactericidal. Preliminary phytochemical tests revealed the presence of tannins, steroids and alkaloids and FT-IR analysis revealed presence of many functional groups namely alcoholic, amide, amine salt and aldehyde groups. From the GC-MS analysis of TLC fraction of ethyl acetate extract, five different bioactive compounds e.g., 2,4-ditert –butylphenyl 5-hydroxypentanoate, Oxalic acid; allyl nonyl ester, 7,9-Ditert-butyl-1-oxaspiro(4,5)deca-6,9-diene- 2,8-dione, Dibutyl phthalate and 2,3,5,8-tetramethyl-decane were identified. Conclusion: Leaf extracts of P. pudica contain bioactive compounds that can be used as broad spectrum bactericidal agent.

Introduction: This study aimed to evaluate the antioxidant property of Silymarin (SM) extracted from the seed of Silybum marianum and its anticancer activity on KB and A549 cell lines following 24, 48, and 72 h of treatment. Methods: Ten grams of powdered S. marianum seeds were defatted using n-hexane for 6 hours and then extracted by methanol. The Silymarin extracted of extraction components. The extracted components of Silymarin were measured by spectrophotometric assay and HPLC analysis. 2, 2- diphenyl-1-picrylhydrazyl (DPPH) radical scavenging, phenol content, total flavonoid content, and total antioxidant capacity were measured to detect the antioxidant properties of SM. The anticancer activity of the SM on cell lines evaluated by MTT. Results: In HPLC analysis, more than 50% of the peaks were related to silybin A and B. SM was reduced DPPH (the stable free radical) with a 50% inhibitory concentration (IC50) of 6.56 μg/ ml in comparison with butylated hydroxyl toluene (BHT), which indicated an IC50 of ~3.9 μg/ ml. The cytotoxicity effect of SM on the cell lines was studied by MTT assay. The cytotoxicity effect of the extracted Silymarin on KB and A549 cell lines was observed up to 80 and 70% at 156 and 78 μg/ml, respectively. The IC50 value of the extracted SM on KB and A549 cell lines after 24 hours of treatment was seen at 555 and 511 μg/ml, respectively. Conclusion: Due to the good antioxidant and anticancer properties of the isolated Silymarin, its use as an anticancer drug is suggested.

Background: Benign prostate hyperplasia [BPH] is an abnormal growth of prostate observed commonly in elderly males. Artemisinin has been reported to reduce the levels of testosterone. Objective: This study is designed to evaluate the efficacy of Artemisinin on testosterone propionate [TP] induced benign prostate hyperplasia. Materials and Methods: Male Wistar albino rats [n=24] were separated into four groups of six rats each. Group I served as control and distilled water using tween 80 as an emulsifying agent was administered subcutaneously. BPH was induced by testosterone propionate 3mg/kg [Group II], S.C. daily for 28 days. Group III was BPH + Finasteride treated group (10mg/kg orally for 28 days) and BPH + Artemisinin treated group (Group IV) (50 mg/kg orally for 28 days). Result: The study results showed significantly high levels of serum prostatic acid phosphatase (PAP), lactate dehydrogenase (LDH) and an elevation in prostate weight and prostatic index in Group II (BPH) when compared with Group I. The histopathological examination showed an increase in the epithelial proliferation of prostatic cells with involutions protruding into the lumen in BPH group when compared to the normal group. Treatment with Artemisinin (50 mg/kg) reduced the levels of PAP, LDH, prostate weight and prostatic index to a significant extent and restored the histoarchitectural features of the cells. Conclusion: The present study concludes that Artemisinin is efficacious in testosterone propionate induced BPH. This could be attributed, at least partly, to its anti-inflammatory property or its role in testosterone level reduction or as a Vitamin D receptor modulator.

Introduction: The present study deals with the effect of Nectaroscordum koelzi fruit extract on acute and chronic inflammation. Methods: A total of 84 NMRI mice were used in this study. The effect of the extract on acute inflammation was analyzed by increasing vascular permeability via acetic acid and xylene induced ear edema among mice. The extract was evaluated in terms of effects on chronic inflammation by means of the cotton pellet test among mice. For the assessment of inflammation degree, the mice paw edema volume was measured by the plethysmometric test. Results: The findings showed that the extract was effective on acute inflammation induced by acetic acid in mice. In the xylene ear edema, N. koelzi extract indicated a significant activity in mice. In the cotton pellet method, the methanol extract produced a significant reduction in comparison with the control and dexamethasone. Mice paw edema volume decreased with the extract. Conclusion: In general, the data from the experiments indicated that the methanol extract of N. koelzi has an anti-inflammatory effect on acute and chronic inflammation. However, the exact contributing mechanisms have not been investigated for the pharmacological effects.

Background: Streptococcus mutans and Streptococcus sanguinis are Gram-positive bacteria that cause dental caries. MurA enzyme acts as a catalyst in the formation of peptidoglycan in bacterial cell walls, making it ideal as an antibacterial target. Basil (Ocimum americanum) is an edible plant that is diverse and has been used as a herbal medicine for a long time. It has been reported that basil has a pharmacological effect as well as antibacterial activity. The purpose of this study was to identify antibacterial compounds in O. americanum and analyze their inhibition activity on MurA enzyme. Methods: Fresh leaves from O. americanum were extracted with n-hexane and purified by a combination of column chromatography on normal and reverse phases together with in vitro bioactivity assay against S. mutans ATCC 25175 and S. sanguinis ATCC 10556, respectively, while in silico molecular docking simulation of lauric acid (1) was conducted using PyRx 0.8. Results: The structure determination of antibacterial compound by spectroscopic methods resulted in an active compound lauric acid (1). The in vitro evaluation of antibacterial activity in compound 1 showed Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) values of 78.13 and 156.3 ppm and 1250 and 2500 ppm against S. sanguinis and S. mutans, respectively. Further analysis and in silico evaluation determined lauric acid (1) as MurA Enzyme inhibitor. Lauric acid (1) showed a binding affinity of -5.2 Kcal/mol, which was higher than fosfomycin. Conclusion: Lauric acid showed the potential as a new natural antibacterial agent through MurA inhibition in bacterial cell wall biosynthesis.

Background: The medicinal plant Myrtus communis L. (Myrtle) has properties, including anti-inflammatory and wound healing in Persian Medicine. Objective: The objective of this study was to explore the wound healing potential of the local application of a gel containing aqueous extract of the plant berry in streptozotocin (STZ)-induced diabetic rats. Methods: Seven days after diabetes establishment, full-thickness excision skin wounds were made in normal and diabetic rats where treated groups received topical application of a gel containing 6% aqueous extract of myrtle berries for 3 weeks. The rate of wound healing and the level of epidermal and dermal maturation in the wound tissue were determined. Results: The results showed that after 3 and 7 days of wound injury, the gel significantly improved wound healing by accelerating epidermal and dermal maturation in diabetic rats with no significant effect in the control group. However, the wounds of all groups almost completely healed after 3 weeks. Conclusion: These results demonstrate that aqueous extract of myrtle possesses a definite wound healing potential in diabetic conditions. The present findings may suggest the use of topical myrtle berries aqueous extract gel 6% to treat and manage intractable diabetic wounds.

Aims: The aim of this study was to investigate the toxic effect of Echium amoenum plants on the liver and kidney of the animal model. Background: Echium amoenum is one of the medicinal plants containing pyrrolizidine alkaloids with several properties which has widely consumed among different communities. Objective: The toxic effects of Echium amoenum on the liver and kidney were investigated in this study. Methods: Sixty mice were kept for 28 days under the appropriate laboratory conditions. Echium amoenum extract (25, 12.5, 50 mg / kg, ip.) was administered for 28 days. At the end of the experiment, blood samples were drawn and liver and kidneys were removed for evaluating hepatotoxicity and nephrotoxicity of extract. Additionally, experiments were conducted to assay the enzymatic and oxidative activities. Results: There was no significant difference in the levels of copper ion in the liver and kidneys among all groups. There was a significant difference in the levels of lipid peroxidation in the liver of treated groups versus the control group. The significant difference was not observed in the levels of glutathione of the liver of all groups. However, the levels of glutathione of the kidney significantly decreased in the treated groups versus the control group. There was no significant difference in the liver enzymes, including ALP, SGOT, and SGPT, between all groups. This indicates that damage increases with enhancing the time and concentrations of the extract. Biochemical analysis showed the creatinine and urea levels did not change in the treated groups versus the control group. Conclusion: According to the present findings, it is suggested that Echium amoenum causes hepatotoxicity and nephrotoxicity effects in dose and time-dependent manner.

Background: In a bid to come up with effective compounds as inhibitors for antimalarial treatment, we built a library of 2,000 traditional Chinese medicine(TCM)-derived compounds retrieved from TCM Database@Taiwan. Methods: The active sites of both the wild type and mutant Plasmodium falciparum dihydrofolatereductase (pfDHFR) were explored using computational tools. pfDHFR, one of the prime drug targets in the prevention of malaria infection induced by the female anopheles mosquito has continued to offer resistance to drugs (antifolates) due to mutation in some of the key amino acid residues crucial for its inhibition. Results: We utilized virtual throughput screening and glide XP docking to screen the compounds, and 8 compounds were found to have promising docking scores with both the wild type and mutant pfDHFR. They were further subjected to Induce Fit Docking (IFD) to affirm their inhibitory potency. The ADME properties and biological activity spectrum of the compounds were also considered. The inhibition profile of the compounds revealed that a number of compounds formed intermolecular interactions with ASP54, ILE14, LEU164, SER108/ASN108, ARG122 and ASP58. Most of the compounds can be considered as drug candidates due to their antiprotozoal activities and accordance with the Lipinski’s Rule of Five (ROF). Conclusion: The outcome of the present study should further be investigated to attest the efficacy of these compounds as better drug candidates than the antifolates.

Introduction: The COVID-19 caused by a new type of coronavirus has emerged from China and led to thousands of deaths globally. Despite many groups engaged in studying the newly emerged virus and searching for the treatment, the understanding of the SARS-CoV2 target ligand interactions represents a key challenge. Several studies are being conducted to identify potential treatment. Alternatively, the results of numerous studies have shown that protease inhibitors can be a genuine leader in research. The antiviral activity and beneficial effect against respiratory disorders of thymoquinone have been largely demonstrated. Aim: The aim of this study is to evaluate in silico the inhibition of the replication of SARS CoV2 by thymoquinone. Methods: This is a molecular simulation study using SARS CoV2 protease and thymoquinone structures provided by Protein Data Bank. Results: The preliminary results have shown that thymoquinone may have inhibitory activities against SARS CoV2 protease. Conclusion: Furthermore, given the demonstrated results of thymoquinone, we can conclude that it may be considered as an effective or adjuvant treatment for SARS CoV2 infection.