Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors.

BACKGROUND: In most parts of the world, especially in underdeveloped countries, acquired immunodeficiency syndrome (AIDS) still remains a major cause of death, disability, and unfavorable economic outcomes. This has necessitated intensive research to develop effective therapeutic agents for the treatment of human immunodeficiency virus (HIV) infection, which is responsible for AIDS. Peptide cleavage by HIV-1 protease is an essential step in the replication of HIV-1. Thus, correct and timely prediction of the cleavage site of HIV-1 protease can significantly speed up and optimize the drug discovery process of novel HIV-1 protease inhibitors. In this work, we built and compared the performance of selected machine learning models for the prediction of HIV-1 protease cleavage site utilizing a hybrid of octapeptide sequence information comprising bond composition, amino acid binary profile (AABP), and physicochemical properties as numerical descriptors serving as input variables for some selected machine learning algorithms. Our work differs from antecedent studies exploring the same subject in the combination of octapeptide descriptors and method used. Instead of using various subsets of the dataset for training and testing the models, we combined the dataset, applied a 3-way data split, and then used a "stratified" 10-fold cross-validation technique alongside the testing set to evaluate the models. RESULTS: Among the 8 models evaluated in the "stratified" 10-fold CV experiment, logistic regression, multi-layer perceptron classifier, linear discriminant analysis, gradient boosting classifier, Naive Bayes classifier, and decision tree classifier with AUC, F-score, and B. Acc. scores in the ranges of 0.91-0.96, 0.81-0.88, and 80.1-86.4%, respectively, have the closest predictive performance to the state-of-the-art model (AUC 0.96, F-score 0.80 and B. Acc. ~ 80.0%). Whereas, the perceptron classifier and the K-nearest neighbors had statistically lower performance (AUC 0.77-0.82, F-score 0.53-0.69, and B. Acc. 60.0-68.5%) at p < 0.05. On the other hand, logistic regression, and multi-layer perceptron classifier (AUC of 0.97, F-score > 0.89, and B. Acc. > 90.0%) had the best performance on further evaluation on the testing set, though linear discriminant analysis, gradient boosting classifier, and Naive Bayes classifier equally performed well (AUC > 0.94, F-score > 0.87, and B. Acc. > 86.0%). CONCLUSIONS: Logistic regression and multi-layer perceptron classifiers have comparable predictive performances to the state-of-the-art model when octapeptide sequence descriptors consisting of AABP, bond composition and standard physicochemical properties are used as input variables. In our future work, we hope to develop a standalone software for HIV-1 protease cleavage site prediction utilizing the linear regression algorithm and the aforementioned octapeptide sequence descriptors.

RHAMNETIN IS A BETTER INHIBITOR OF SARS-COV-2 2'-O-METHYLTRANSFERASE THAN DOLUTEGRAVIR: A COMPUTATIONAL PREDICTION.

Background: The 2'-O-methyltransferase is responsible for the capping of SARS-CoV-2 mRNA and consequently the evasion of the host's immune system. This study aims at identifying prospective natural inhibitors of the active site of SARS-CoV-2 2'O-methyltransferase (2'-OMT) through an in silico approach. Materials and methods: The target was docked against a library of natural compounds obtained from edible African plants using PyRx - virtual screening software. The antiviral agent, Dolutegravir which has a binding affinity score of -8.5 kcal mol-1 with the SARS-CoV-2 2'-OMT was used as a standard. Compounds were screened for bioavailability through the SWISSADME web server using their molecular descriptors. Screenings for pharmacokinetic properties and bioactivity were performed with PKCSM and Molinspiration web servers respectively. The PLIP and Fpocket webservers were used for the binding site analyses. The Galaxy webserver was used for simulating the time-resolved motions of the apo and holo forms of the target while the MDWeb web server was used for the analyses of the trajectory data. Results: The Root-Mean-Square-Deviation (RMSD) induced by Rhamnetin is 1.656A0 compared to Dolutegravir (1.579A0). The average B-factor induced by Rhamnetin is 113.75 while for Dolutegravir is 78.87; the Root-Mean-Square-Fluctuation (RMSF) for Rhamnetin is 0.75 and for Dolutegravir is 0.67. Also, at the active site, Rhamnetin also has a binding affinity score of -9.5 kcal mol-1 and forms 7 hydrogen bonds compared to Dolutegravir which has -8.5 kcal mol-1 and forms 4 hydrogen bonds respectively. Conclusion: Rhamnetin showed better inhibitory activity at the target's active site than Dolutegravir.

Study of the Antimalarial Activity of the Leaf Extracts and Fractions of Persea americana and Dacryodes edulis and Their HPLC Analysis.

In the present study, the antimalarial activity of the extracts and fractions of the leaves of Persea americana and Dacryodes edulis as well as their phytochemical compositions were examined. Each of the extracts of the plants was successively fractionated to obtain hexane, ethyl acetate, methanol, and water fractions. The extracts and fractions were tested against Plasmodium berghei in both curative and suppressive antimalarial mouse models. Their major phytochemical composition was studied by the standard chemical tests and HPLC analysis. The extracts and fractions of P. americana and D. edulis demonstrated significant (p < 0.05) maximal plasmodial inhibition as 52.16 ± 2.77% and 57.10 ± 1.98%, respectively, and chemosuppression of parasitemia as 64.01 ± 0.08% and 71.99 ± 0.06%, respectively. The major secondary metabolites identified in the plants include alkaloids, flavonoids, and saponins. It was concluded that P. americana and D. edulis possess promising antimalarial activity and they are potential sources of new lead compounds against malaria.

Alkaloids from Plants with Antimalarial Activity: A Review of Recent Studies.

Malaria is one of the major health problems in developing countries. The disease kills a large number of people every year and also affects financial status of many countries. Resistance of the plasmodium parasite, the causative agent, to the existing drugs, including chloroquine, mefloquine, and artemisinin based combination therapy (ACT), is a serious global issue in malaria treatment and control. This warrants an urgent quest for novel compounds, particularly from natural sources such as medicinal plants. Alkaloids have over the years been recognized as important phytoconstituents with interesting biological properties. In fact, the first successful antimalarial drug was quinine, an alkaloid, which was extracted from Cinchona tree. In the present review work, the alkaloids isolated and reported recently (2013 till 2019) to possess antimalarial activity are presented. Several classes of alkaloids, including terpenoidal, indole, bisindole, quinolone, and isoquinoline alkaloids, were identified with a promising antimalarial activity. It is hoped that the reports of the review work will spur further research into the structural modification and/or development of the interesting compounds as novel antimalarial drugs.

Medicinal plants used by the people of Nsukka Local Government Area, south-eastern Nigeria for the treatment of malaria: An ethnobotanical survey.

ETHNOBOTANICAL RELEVANCE: Malaria is a serious public health problem especially in sub-Saharan African countries such as Nigeria. The causative parasite is increasingly developing resistance to the existing drugs. There is urgent need for alternative and affordable therapy from medicinal plants which have been used by the indigenous people for many years. AIM OF STUDY: This study was conducted to document the medicinal plant species traditionally used by the people of Nsukka Local Government Area in south-eastern Nigeria for the treatment of malaria. METHODS: A total of 213 respondents, represented by women (59.2%) and men (40.8%), were interviewed using a semi-structured questionnaire. The results were analysed and discussed in the context of previously published information on anti-malarial and phytochemical studies of the identified plants. RESULTS: The survey revealed that 50 plant species belonging to 30 botanical families were used in this region for the treatment of malaria. The most cited families were Apocynaceae (13.3%), Annonaceae (10.0%), Asteraceae (10.0%), Lamiaceae (10.0%), Poaceae (10.0%), Rubiaceae (10.0%) and Rutaceae (10.0%). The most cited plant species were Azadirachta indica (11.3%), Mangifera indica (9.1%), Carica papaya (8.5%), Cymbopogon citratus (8.5%) and Psidium guajava (8.5%). CONCLUSION: The present findings showed that the people of Nsukka use a large variety of plants for the treatment of malaria. The identified plants are currently undergoing screening for anti-malarial, toxicity and chemical studies in our laboratory.

Antidiabetic Activity of Extract and Compounds from an Endophytic Fungus Nigrospora oryzae.

The fungal extract as well as the 3 biosynthetic compounds, (S)-(+)-2-cis-4-trans-abscisic acid (1), , 7'-hydroxy-abscisic acid (2) and 4-des-hydroxyl altersolanol A (3) from the endophytic fungus, Nigrospora oryzae, isolated from Combretum dolichopetalum leaf were investigated for their antidiabetic potential.The antidiabetic activity was determined in alloxan-induced diabetic mice by monitoring their fasting blood sugar for 9 h.The extract and the compounds (1-3) significantly (p<0.001) reduced the fasting blood sugar of the diabetic mice.The present study has shown that the biosynthetic products of the endophytic fungus, N. oryzae, exhibited strong antidiabetic activity. It has further shown that endophytic fungi could be an alternative source of novel compounds for management of diabetes.

Antidiabetic activity of the chemical constituents of Combretum dolichopetalum root in mice.

The root of Combretum dolichopetalum (Combreatacea) is used in ethnomedicine for the management of diabetes mellitus. Though some compounds have been isolated from it, the antidiabetic principles have not been identified. The present study was designed to evaluate the chemical constituents from the root of C. dolichopetalum with a view to identifying the antidiabetic principles. The constituents include the alkaloids, echinulin (1) and arestrictin B (2), the terpenoids, arjunolic acid (3) and 4'-dihydrophaseic acid (4) as well as the phenolic acids, ellagic acid (5) and 3, 4, 3'-tri-O-methylellagic acid (6). Twenty eight mice (in seven groups, n = 4) were made diabetic using alloxan monohydrate (i.p., 120 mg/kg) and treated orally with either the vehicle (control group), any of the constituents or glibenclamide (standard drug). The fasting blood glucose of the diabetic animals was monitored for nine hours. Results showed that all the chemical constituents (1-6) exhibited significant (p < 0.05) antidiabetic activity comparable to glibenclamide. The alkaloids exhibited the most profound antidiabetic activity. The present study has thus identified the antidiabetic principles of C. dolichopetalum root as echinulin, arestrictin B, arjunolic acid, 4'-dihydrophaseic acid, ellagic acid and 3, 4, 3'-tri-O-methylellagic acid. The study has further validated the ethnomedicinal use of the root of C. dolichopetalum in diabetes.

Metabolites from Combretum dolichopetalum and its associated endophytic fungus Nigrospora oryzae--Evidence for a metabolic partnership.

A new altersolanol derivative, 4-dehydroxyaltersolanol A (9), along with two known sesquiterpenoids, (S)-7'-hydroxyabscisic acid (7) and (S)-abscisic acid (8) were obtained from the endophytic fungus, Nigrospora oryzae, isolated from leaves of Combretum dolichopetalum. The host plant yielded six known compounds including ellagic acid (1), 3, 3', 4-tri-O-methylellagic acid (2), arjunolic acid (3), 4'-dihydrophaseic acid (4), echinulin (5) and arestrictin B (6). Close structural similarities with regard to compounds 4, 7 and 8 were observed between the metabolites from the host plant and those of the endophytic fungus. Furthermore compounds 5 and 6 are related to alkaloids isolated from N. oryzae previously thus stressing the notion that some of the isolated plant metabolites may actually be of fungal origin. The structures of the isolated compounds were established by spectroscopic methods including 1D, 2D NMR, MS, and by comparison with the literature. 4-Dehydroxyaltersolanol A (9) and 3, 3', 4-tri-O-methylellagic acid (2) showed cytotoxicity against L5178Y mouse lymphoma cells with IC50 values of 9.4 and 29.0 µM, respectively.

Immunomodulatory effects of Stachytarpheta cayennensis leaf extract and its synergistic effect with artesunate.

BACKGROUND: The leaves of Stachytarpheta cayennensis C. Rich. (Verbenaceae) have been reported to possess potent anti-inflammatory and anti-malarial activities. Due to close association between inflammatory and immune responses, we evaluated the immunomodulatory activity of leaves extract of S. cayennensis. The combined effects of the leaves extract and artesunate, a standard antimalarial agent with immunomodulatory effects, were also evaluated. METHODS: The immunomodulatory activity of the methanol extract of the leaves of S. cayennensis (MESC) was evaluated in mice using the Delayed-Type hypersensitivity response (DTHR), primary and secondary humoral immune responses and the in vivo leucocyte mobilization tests. The immunomodulatory effect of artesunate and the combined effects of MESC and artesunate were evaluated using the phagocytic activity of polymorphonuclear neutrophils. Acute toxicity and lethality test in addition to the preliminary phytochemical studies of MESC were also performed. RESULTS: The MESC exhibited 64.21% inhibition of DTHR at 500 mg/kg dose and evoked 139.64% of phagocytic stimulation at 100 µg/ml dose. Also MESC significantly (p < 0.05) showed dose related stimulation of humoral immunity and a highest percentage leucocyte mobilization of 10.15% at 250 mg/kg dose. Artesunate offered a non-significant (p > 0.05) percentage phagocytic stimulation (PPS) while the combined effect of artesunate and MESC exhibited a significant (p < 0.05) dose dependent PPS with highest PPS of 393.77% at 100 µg/ml. The LD50 of the MESC was estimated to be greater than 5000 mg/kg since there were no lethality and signs of acute intoxication after 48 h observation. Preliminary phytochemical analysis revealed the presence of carbohydrates, glycosides, flavonoids, saponins, alkaloids, terpenoids and steroids. CONCLUSIONS: The results of this study indicated that MESC possesses immunostimulatory action with significant synergistic effects with artesunate, and can therefore, offer immune boosting activities in disorders of immune suppression.

Phytochemical analysis, hepatoprotective and antioxidant activity of Alchornea cordifolia methanol leaf extract on carbon tetrachloride-induced hepatic damage in rats.

OBJECTIVE: To investigate the hepatoprotective and antioxidant activities of Alchornea cordifolia (A. cordifolia) leaf extract. METHODS: Various solvent fractions of the methanol extract of the leaf of the plant A. cordifolia Mull. Arg (Fam: Euphorbiaceae) were evaluated for hepatoprotective activity by carbon tetrachloride-induced liver damage in rats. The degree of protection was measured by using biochemical parameters such as serum glutamate oxalate transaminase (SGOT/AST), serum glutamate pyruvate transaminase (SGPT/ALT), alkaline phosphatase (ALP) and total bilirubin. The in vitro antioxidant activity of the extract was also evaluated by the 1, 1-diphenyl- 2-picrylhydrazyl (DPPH) free radical scavenging assay. The extract was subjected to preliminary phytochemical screening. RESULTS: The ethyl acetate and chloroform fractions, at a dose of 300 mg/kg, produced significant (P<0.05) hepatoprotection by decreasing the activities of the serum enzymes and bilirubin while there were marked scavenging of the DPPH free radicals by the fractions. The effects were comparable to those of the standard drugs used for the respective experiments, silymarin and ascorbic acid. Alkaloids, flavonoids, saponins and tannins were detected in the phytochemical screening. CONCLUSION: From this study, it was concluded that the plant of A. cordifolia possesses hepatoprotective as well as antioxidant activities and these activities reside mainly in the ethyl acetate and acetone fractions of methanol leaf extract.