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Abstract

The process of drug discovery is considered as one of the longest and costliest efforts. The classical approach to drug discovery process is the identification of drug target, then designing the lead compound, and finally the validation of the compounds through clinical trials. It was considered that on an average one new drug takes approximately 12-13 years to reach to a patient from a research laboratory. Millions have been spent to find some new drug candidates for the particular disease, but the success rate is very low. The reason could be the limited knowledge of complex biological systems. Therefore, it was perceived that until in-depth knowledge of the complex biological process that leads to the diseased state is considered, the discovery of new drug will be a time-consuming and challenging process. Well known compounds have been discovered by serendipity. The best-known drug is Artemisinin, the present frontline drug for treatment of Malaria. Many combinatorial substitutions have been synthesized and inhibition was tested for more than 100 compounds, analogs of Artemisinin, but the single target has yet not been identified. So the widespread promiscuity about its mechanism of action is a challenge to designing better compound from this. Recent studies are shown the resistance is also growing, which can only be resolved if the actual binding target is known. In search for the plausible mechanism of action, a calcium pump called PfATP6 has been investigated to understand the role of iron and Artemisinin on PfATP6 and compared with human homolog protein. During the binding, a closure between different domain like phosphorylation, nucleotide binding and actuator domains happen, this stops Ca⁺⁺ to enter and the loss of function of PfATP6. Comparing the human Ca⁺⁺/ATPase (SERCA), it was found that such activity is not possible, which reflects in low IC50 of binding of Artemisinin to human. An attempt has been made to design appropriate Pharmacophore model using available Artemisinin analogs and the binding to the open and close conformation of calcium pump PfATP6. Two different methods have been used to develop diverse pharmacophore features that may be utilized for either screening databases for non-sesquiterpene lactone scaffold based inhibitor identification or probing the role of flexibility by docking the pharmacophore features in the binding site of the target protein. The present study will provide validation of such mechanism and help in the design of novel antimalarial. Many tools like density functional theory calculations, pharmacophore generation, docking and molecular dynamics simulations are used efficiently to find that Artemisinin gets activated in the presence of iron and then only can inhibit PfATP6.

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... By clustering, 11 representative structures of PfATPase6 are determined and used to understand the dynamic interaction profile by combinatorial docking of the 23 pharmacophore features (Kumar et al., 2017) and Fig. 14.7C shows the docking score for corresponding features set at the y-axis. This analysis emphasizes the role of domain movements and taking care of flexibility in the drug-binding site. ...
Chapter
The recent advancements of machine learning and deep learning (DL) methods are making it possible to create systems that automatically mine patterns and learn from data. Applications of those methods in chemistry, in particular QSAR and drug discovery, are already available. While DL can be applied as a conventional way of learning from chemical descriptors, the potentialities of the method are far more. In particular the capabilities of DL to autonomously extract, through multiple transformations, the structural elements that are correlated with the property under investigation can help in discovering the link between a chemical and its biological/physical effects. After presenting the principal DL methods developed for chemical problems, the focus is on a study case in mutagenicity prediction that uses directly the chemical graph, either as SMILES, graphs, or images, and applies convolutional and recurrent networks. The knowledge extracted from the networks is analyzed and compared with the accepted structural alerts for mutagenicity. The next challenges and the future of DL for QSAR are finally discussed.
... By clustering, 11 representative structures of PfATPase6 are determined and used to understand the dynamic interaction profile by combinatorial docking of the 23 pharmacophore features (Kumar et al., 2017) and Fig. 14.7C shows the docking score for corresponding features set at the y-axis. This analysis emphasizes the role of domain movements and taking care of flexibility in the drug-binding site. ...
Chapter
In this chapter, we have discussed a relatively advanced and successful hybrid machine learning workflow that may help to unravel causative agents of disease from high throughput RNA-Seq datasets. The method is then applied to a breast cancer dataset taken from the Gene Expression Omnibus repository, and disease genes associated with breast cancer are identified. Finally, using the PPI network analysis approach, we observed the significance that the detected disease genes possess a role in the causal mechanism of disease. This method discussed here is universal and can be applied to any RNA-Seq data independent of disease.
... Artemisinin adduct binds in the membrane-bound helical region and makes a hydrogen bond network which connects it with extracellular nucleotide [91]. This case study shows the selectivity gain by bound inhibitor, utilizing the domain flexibility of receptor [94]. ...
Chapter
Structure-based in silico studies aiming to predict affinity of a set of ligands to their cognate receptor have been enjoying keen interest and attention of researchers in drug design around the globe since many decades, and made significant progress to increase its predictive power, even it has emerged as a complementary field to in vivo and in vitro studies in recent years. Structure-based drug discovery (SBDD) process whose success heavily relies on a careful selection of structure of receptor and ligands and its accuracy, completeness, and rigor of chosen model, imitation of the physiological condition in such in silico models, e.g., pH and solvation. Appropriateness of selected mechanism of binding concept and the realization in mathematical terms used in scoring methods have a strong influence on the accuracy too. However, constant identification of new targets using systems approach like genomics, proteomics, metabolomics, and network biology has led a paradigm shift from single or a couple of targets toward the appreciation of emerging role of a network of targets. The application of such strategies in study of complex diseases is gaining attention. Identification of binding sites of receptor and their characterization is important to be able to portray its interacting features. It involves the search of ligands which are able to possess the features, present them complementary to the binding site, so by docking the set of ligands to the binding pocket of the receptor, activity can be evaluated. In silico receptor–ligand binding affinity prediction from docking has witnessed rigid-receptor rigid-ligand to flexible-ligand rigid-receptor treatment, and nowadays docking studies, through sampling side chain rotations of the binding site residues, also account for the flexibility of binding pocket of the receptor in indirect way. Literature survey has shown progress in ranking ligands in order of affinity using reliable scoring functions to find potent scaffolds which can be further optimized to gain more affinity. Many methods include effect of solvation in binding processes, like considering conserved water positions in active sites (water maps), explicit water simulation in presence of ligand with receptor, free energy perturbation, and thermodynamic integration. Availability of many conformers of receptors and ligands in solution suggests the importance of entropy in estimation of binding affinity, but entropy component of binding free energy directly is not included in such studies. In spite of unprecedented advancement of computational modeling, faster simulation techniques, accurate solvation models and current best practices, the dependence of binding affinity on pH, estimation of entropy along with enthalpy in binding affinity, inclusion of conformational entropy of ligand and receptor, and modulation of flexibilities during complex formation are important challenges lying ahead. Therefore, an account of prowess and challenges in structure-based prediction of binding affinity addressed in present review will provide directions for its appropriate application, understanding its limitations and getting important feedbacks for its betterment.
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Needless to say that cure from malaria disease is a longstanding goal and helping the present worldwide effort to reduce the malarial disease burden by many folds. Chloroquine (CQ) and Artemisinin (ART) antimalarial drugs are among the most successful in treating malaria; however, CQ-resistant Plasmodium species are now at every corner of the malarial epidemic regions, while ART resistance is upcoming. Pharmacophore features derived from both drugs can be implemented to overcome the growing resistance as well as designing multi-targeted novel non-Chloroquine and non-Artemisinin scaffolds containing inhibitors. In the present study, two different pharmacophore modeling approaches are used to understand the pharmacophore feature distribution between the CQ-Sensitive and CQ-Resistance analogs. To exclude the possible resistance-causing features for CQ, a subtractive pharmacophore modeling protocol has been illustrated and further optimized to a CQ model which is used to screen novel antimalarial inhibitors. Along with CQ, Artemisinin analogs are also used for pharmacophore modeling and additive pharmacophore modeling has been implemented for novel antimalarials designing. We have discussed and used these models for searching novel inhibitors. The subtractive model is used to identify non-CQ scaffolds containing inhibitors while the additive model is used to design the non-ART & non-CQ scaffold containing inhibitors by chemical mining approach to overcome malarial resistance
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Abstract The Millennium Development Goals (MDGs) made a marked transformation for neglected and vulnerable communities in the developing countries from the start, but infectious diseases of poverty (IDoPs) continue to inflict a disproportionate global public health burden with associated consequences, thereby contributing to the vicious cycle of poverty and inequity. However, the effectiveness and large-scale coverage of artemisinin combination therapy (ACT) have revolutionized malaria treatment just as the control of lymphatic filariasis (LF) and onchocerciasis have benefitted from harnessing the broad-spectrum effect of avermectin-based derivatives. The paradigm shift in therapeutic approach, effected by these two drugs and their impact on community-based interventions of parasitic diseases plaguing the endemic low- and middle-income countries (LIMCs), led to the Nobel Prize in Physiology or Medicine in 2015. However, the story would not be complete without mentioning praziquantel. The huge contribution of this drug in modernizing the control of schistosomiasis and also some intestinal helminth infections had already shifted the focus from control to potential elimination of this disease. Together, these new drugs have provided humankind with powerful new tools for the alleviation of infectious diseases that humans have lived with since time immemorial. These drugs all have broad-spectrum effects, yet they are very safe and can even be packaged together in various combinations. The strong effect on so many of the great infectious scourges in the developing countries has not only had a remarkable influence on many endemic diseases, but also contributed to improving the cost structure of healthcare. Significant benefits include improved quality of preventive and curative medicine, promotion of community-based interventions, universal health coverage and the fostering of global partnerships. The laudable progress and benefits achieved are indispensable in championing, strengthening and moving forward elimination of the IDoPs. However, there is an urgent need for further innovative, contextual and integrated approaches along with the advent of the Sustainable Development Goals (SDGs), replacing the MDGs in ensuring global health security, well-being and economic prosperity for all. Keywords: Nobel Prize, Artemisinin, Avermectin, Ivermectin, Praziquantel, Schistosomiasis, Intestinal helminths, Lymphatic filariasis, River blindness, Malaria, Discovery, Poverty
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Antimalarial drugs are key tools for the control and elimination of malaria. Recent decreases in the global malaria burden are likely due, in part, to the deployment of artemisinin-based combination therapies. Therefore, the emergence and potential spread of artemisinin-resistant parasites in southeast Asia and changes in sensitivities to artemisinin partner drugs have raised concerns. In recognition of this urgent threat, the International Centers of Excellence for Malaria Research (ICEMRs) are closely monitoring antimalarial drug efficacy and studying the mechanisms underlying drug resistance. At multiple sentinel sites of the global ICEMR network, research activities include clinical studies to track the efficacies of antimalarial drugs, ex vivo/in vitro assays to measure drug susceptibilities of parasite isolates, and characterization of resistance-mediating parasite polymorphisms. Taken together, these efforts offer an increasingly comprehensive assessment of the efficacies of antimalarial therapies, and enable us to predict the emergence of drug resistance and to guide local antimalarial drug policies. Here we briefly review worldwide antimalarial drug resistance concerns, summarize research activities of the ICEMRs related to drug resistance, and assess the global impacts of the ICEMR programs. © The American Society of Tropical Medicine and Hygiene.
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Artemisinin constitutes the frontline treatment to aid rapid clearance of parasitaemia and quick resolution of malarial symptoms. However, the widespread promiscuity about its mechanism of action is baffling. There is no consensus about the biochemical target of artemisinin but recent studies implicate haem and PfATP6 (a calcium pump). We investigated the role of iron and artemisinin on PfATP6, in search of a plausible mechanism of action, via density functional theory calculations, docking and molecular dynamics simulations. Results suggest that artemisinin gets activated by iron which in turn inhibits PfATP6 by closing the phosphorylation, nucleotide binding and actuator domains leading to loss of function of PfATP6 of the parasite and its death. The mechanism elucidated here should help in the design of novel antimalarials.
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This handbook is the first to address the practical aspects of this novel method. It provides a complete overview of the field and progresses from general considerations to real life scenarios in drug discovery research. Starting with an introductory historical overview, the authors move on to discuss ligand-based approaches, including 3D pharmacophores and 4D QSAR, as well as the concept and application of pseudoreceptors. The next section on structure-based approaches includes pharmcophores from ligand-protein complexes, FLIP and 3D protein-ligand binding interactions. The whole is rounded off with a complete section devoted to applications and examples, including modeling of ADME properties. With its critical evaluation of pharmacophore-based strategies, this book represents a valuable aid for project leaders and decision-makers in the pharmaceutical industry, as well as pharmacologists, and medicinal and chemists.
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We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
Article
The pharmacophore concept is of central importance in computer-aided drug design (CADD) mainly because of its successful application in medicinal chemistry and, in particular, high-throughput virtual screening (HTVS). The simplicity of the pharmacophore definition enables the complexity of molecular interactions between ligand and receptor to be reduced to a handful set of features. With many pharmacophore screening softwares available, it is of the utmost interest to explore the behavior of these tools when applied to different biological systems. In this work, we present a comparative analysis of eight pharmacophore screening algorithms (Catalyst, Unity, LigandScout, Phase, Pharao, MOE, Pharmer, and POT) for their use in typical HTVS campaigns against four different biological targets by using default settings. The results herein presented show how the performance of each pharmacophore screening tool might be specifically related to factors such as the characteristics of the binding pocket, the use of specific pharmacophore features, and the use of these techniques in specific steps/contexts of the drug discovery pipeline. Algorithms with rmsd-based scoring functions are able to predict more compound poses correctly as overlay-based scoring functions. However, the ratio of correctly predicted compound poses versus incorrectly predicted poses is better for overlay-based scoring functions that also ensure better performances in compound library enrichments. While the ensemble of these observations can be used to choose the most appropriate class of algorithm for specific virtual screening projects, we remarked that pharmacophore algorithms are often equally good, and in this respect, we also analyzed how pharmacophore algorithms can be combined together in order to increase the success of hit compound identification. This study provides a valuable benchmark set for further developments in the field of pharmacophore search algorithms, e.g., by using pose predictions and compound library enrichment criteria.
Article
This article introduces several methods of assessing the extent to which a collection of conformations represents or covers conformational space. It also describes poling: a novel technique for promoting conformational variation that can be applied to any method of conformational analysis that locally minimizes a penalty or energy function. The function being minimized is modified to force similar conformers away from each other. The method is independent of the origin of the initial conformers and of the particular minimization method used. It is found that, with the modification of the penalty function, clustering of the resulting conformers is generally unnecessary because the conformers are forced to be dissimilar. The functional form of the poling function is presented, and the merits are discussed with reference to (1) efficacy at promoting variation and (2) perturbation of the unmodified function. Results will be presented using conformers obtained from distance geometry with and without poling. It will be shown that the addition of poling eliminates much redundancy in conformer generation and improves the coverage of the conformational space. © 1995 by John Wiley & Sons, Inc.
Article
The AM1-BCC method quickly and efficiently generates high-quality atomic charges for use in condensed-phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6-31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O-, N-, and S-containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1-BCC yields charge sets of comparable quality to HF/6-31G* ESP-derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP-fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d-glucose, and eryodictyol; the AM1-BCC model again provides atomic charges of quality comparable with HF/6-31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root-mean-square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1-BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000
Article
Novel C4-(hydroxyalkyl)trioxanes 5d and 5e were designed and synthesized based on an understanding of the molecular mechanism of action of similar 1,2,4-trioxanes structurally related to the antimalarial natural product artemisinin (1). In vitro efficacies of these two new pairs of C4-diastereomers against chloroquine-sensitive Plasmodium falciparum support conclusions about the importance to antimalarial activity of formation of a C4 radical by a 1,5-hydrogen atom abstraction. Derivatives 6, 7, and 21 of C4 beta-substituted trioxane alcohols 4a, 5d, and 5e were prepared, each in a single-step, high-yielding transformation. Four of these new analogues, 6a-c and 7, are potent in vitro antimalarials, having 140 to 50% of the efficacy of the natural trioxane artemisinin (1).
Article
On the basis of a mechanistic understanding of the mode of action of artemisinin-like antimalarials, a series of structurally simple 3-aryl-1,2,4-trioxanes 5 was designed and was prepared in three to five operations from commercial reactants. The 3-aryl group was attached in each case as a nucleophile. In an electronically complementary fashion, 3-(fluoroalkyl)-trioxanes 6 were prepared via attachment of electrophilic fluoroalkyl esters. Both in vitro and in vivo antimalarial evaluations of these new trioxanes showed 12 beta-methoxy-3-aryltrioxanes 5g, 5j, 5k, and 51 to be highly potent, with crystalline fluorobenzyl ether trioxane 5k especially potent even when administered to rodents orally. As shown by rearrangement of hexamethyl Dewar benzene into hexamethylbenzene, iron-induced degradation of some of these 3-aryltrioxanes 5 involves generation of high-valent iron oxo species that might kill malaria parasites.
Article
Resistance to antimalarial drugs has often threatened malaria elimination efforts and historically has led to the short-term resurgence of malaria incidences and deaths. With concentrated malaria eradication efforts currently underway, monitoring drug resistance in clinical settings complemented by in vitro drug susceptibility assays and analysis of resistance markers, becomes critical to the implementation of an effective antimalarial drug policy. Understanding of the factors, which lead to the development and spread of drug resistance, is necessary to design optimal prevention and treatment strategies. This review attempts to summarize the unique factors presented by malarial parasites that lead to the emergence and spread of drug resistance, and gives an overview of known resistance mechanisms to currently used antimalarial drugs.
Article
Plasmodium falciparum, the most virulent of the human malaria parasites, causes up to one million deaths per year. The parasite spends part of its lifecycle inside the red blood cells (RBCs) of its host. As it grows it ingests the RBC cytoplasm, digesting it in an acidic vacuole. Free haem released during haemoglobin digestion is detoxified by conversion to inert crystals of haemozoin. Malaria pathology is evident during the blood stage of the infection and is exacerbated by adhesion of infected RBCs to blood vessel walls, which prevents splenic clearance of the infected cells. Cytoadherence is mediated by surface-exposed virulence proteins that bind to endothelial cell receptors. These 'adhesins' are exported to the RBC surface via an exomembrane system that is established outside the parasite in the host cell cytoplasm. Antimalarial drugs that interfere with haem detoxification, or target other parasite-specific processes, have been effective in the treatment of malaria, but their use has been dogged by the development of resistance. Similarly, efforts to develop an effective blood vaccine are hindered by the variability of surface-exposed antigens.
Article
With the advent of artemisinin resistance, it is timely to revisit the biological basis for the controversial suggestion that this class of antimalarial exerts its activity by inhibiting a calcium ATPase (PfATP6) that is most similar to sarcoplasmic endoplasmic reticulum calcium ATPases (SERCAs). Herein, evidence is discussed that relates to this hypothesis as alternative suggestions for how artemisinins might act have been reviewed elsewhere.
Article
Pharmacophore approaches have become one of the major tools in drug discovery after the past century's development. Various ligand-based and structure-based methods have been developed for improved pharmacophore modeling and have been successfully and extensively applied in virtual screening, de novo design and lead optimization. Despite these successes, pharmacophore approaches have not reached their expected full capacity, particularly in facing the demand for reducing the current expensive overall cost associated with drug discovery and development. Here, the challenges of pharmacophore modeling and applications in drug discovery are discussed and recent advances and latest developments are described, which provide useful clues to the further development and application of pharmacophore approaches.
Article
Worldwide spread of Plasmodium falciparum drug resistance to conventional antimalarials, chloroquine and sulfadoxine/pyrimethamine, has been imposing a serious public health problem in many endemic regions. Recent discovery of drug resistance-associated genes, pfcrt, pfmdr1, dhfr, and dhps, and applications of microsatellite markers flanking the genes have revealed the evolution of parasite resistance to these antimalarials and the geographical spread of drug resistance. Here, we review our recent knowledge of the evolution and spread of parasite resistance to chloroquine and sulfadoxine/pyrimethamine. In both antimalarials, resistance appears to be largely explained by the invasion of limited resistant lineages to many endemic regions. However, multiple, indigenous evolutionary origins of resistant lineages have also been demonstrated. Further molecular evolutionary and population genetic approaches will greatly facilitate our understanding of the evolution and spread of parasite drug resistance, and will contribute to developing strategies for better control of malaria.
Article
Artemisinin (qinghaosu), is a promising new antimalarial drug derived from an ancient Chinese herbal remedy. When [13-14C]artemisinin is added to cultures of Plasmodium falciparum, it is converted into a product with different solubility and chromatographic properties than the parent drug. Artemisinin reacts with hemin in aqueous solution to form an adduct with an apparent molecular weight of 914 which has identical chromatographic, solubility, and electrophoretic behavior to the parasite-derived product. The reaction between artemisinin and hemin, when carried out in the presence of red cell membranes, leads to the oxidation of protein thiols. Malarial parasites are rich in hemin; artemisinin's reactivity toward hemin may explain its selective toxicity to malarial parasites.
Article
The antimalarial activity of a series of synthetic 1,2,4-trioxanes is correlated with molecular structure by using a pharmacophore search method (CATALYST). The technique is shown to have predictive accuracy and confirms that docking between an active trioxane and the receptor, heme, is the crucial step for drug action.
Article
In only three chemical operations, natural trioxane lactone artemisinin (1) was converted into a series of C-10 carbon-substituted 10-deoxoartemisinin compounds 4-9. The three steps involved lactone reduction, replacement of the anomeric lactol OH by F using diethylaminosulfur trifluoride, and finally boron trifluoride-promoted substitution of F by aryl, heteroaryl, and acetylide nucleophiles. All of these C-10 nonacetal, chemically robust, enantiomerically pure compounds 4-9 have high antimalarial potencies in vitro against Plasmodium falciparum malaria parasites, and furans 5a and 5b and pyrrole 7a are antimalarially potent also in vivo even when administered to rodents orally.
Article
Artemisinins have been used since ancient times to treat malaria. A new theory could explain how this age-old medicine is able to cause the death of the malaria parasite.
Article
We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.
Article
Evidence is reviewed elucidating the mechanism of iron-induced triggering of antimalarial trioxanes. As prodrugs, trioxanes undergo homolytic, inner-sphere, reductive cleavage by ferrous iron to form sequentially oxy radicals, carbon radicals, high-valent iron-oxo species, epoxides, aldehydes, and dicarbonyl compounds. One or more of these reactive intermediates and neutral alkylating agents likely kill the malaria parasites. Several new, orally active antimalarial peroxides have been designed rationally based on this fundamental mechanistic paradigm. Incorporating metabolism-blocking substituents also provides some new, potent, semi-synthetic artemisinin derivatives.
Article
The discovery of artemisinin more than 30 years ago provided a completely new antimalarial structural prototype; that is, a molecule with a pharmacophoric peroxide bond in a unique 1,2,4-trioxane heterocycle. Available evidence suggests that artemisinin and related peroxidic antimalarial drugs exert their parasiticidal activity subsequent to reductive activation by haem, released as a result of haemoglobin digestion by the malaria-causing parasite. This irreversible redox reaction produces carbon-centred free radicals, leading to alkylation of haem and proteins (enzymes), one of which--the sarcoplasmic-endoplasmic reticulum ATPase PfATP6 (ref. 7)--may be critical to parasite survival. Notably, there is no evidence of drug resistance to any member of the artemisinin family of drugs. The chemotherapy of malaria has benefited greatly from the semi-synthetic artemisinins artemether and artesunate as they rapidly reduce parasite burden, have good therapeutic indices and provide for successful treatment outcomes. However, as a drug class, the artemisinins suffer from chemical (semi-synthetic availability, purity and cost), biopharmaceutical (poor bioavailability and limiting pharmacokinetics) and treatment (non-compliance with long treatment regimens and recrudescence) issues that limit their therapeutic potential. Here we describe how a synthetic peroxide antimalarial drug development candidate was identified in a collaborative drug discovery project.
Article
Artemisinins form the most important class of antimalarial currently available, particularly because they are effective against parasites resistant to almost all the other classes. Their mechanism of action is controversial. Some aspects of this controversy are reviewed here. Whilst there is no clinical resistance yet identified to artemisinins, the potential to examine the relationship between polymorphisms in PfATP6 (a target of artemisinins) in multidrug resistant isolates of Plasmodium falciparum, is also discussed.