Development and application of fragment-based de novo inhibitor design approaches against Plasmodium falciparum GST.

CONTEXT: Modulation of disease progression is frequently started by identifying biochemical pathway catalyzed by biomolecule that is prone to inhibition by small molecular weight ligands. Such ligands (leads) can be obtained from natural resources or synthetic libraries. However, de novo design based on fragments assembly and optimization is showing increasing success. Plasmodium falciparum parasite depends on glutathione-S-transferase (PfGST) in buffering oxidative heme as an approach to resist some antimalarials. Therefore, PfGST is considered an attractive target for drug development. In this research, fragment-based approaches were used to design molecules that can fit to glutathione (GSH) binding site (G-site) of PfGST. METHODS: The involved approaches build molecules from fragments that are either isosteric to GSH sub-moieties (ligand-based) or successfully docked to GSH binding sub-pockets (structure-based). Compared to reference GST inhibitor of S-hexyl GSH, ligands with improved rigidity, synthetic accessibility, and affinity to receptor were successfully designed. The method involves joining fragments to create ligands. The ligands were then explored using molecular docking, Cartesian coordinate's optimization, and simplified free energy determination as well as MD simulation and MMPBSA calculations. Several tools were used which include OPENEYE toolkit, Open Babel, Autodock Vina, Gromacs, and SwissParam server, and molecular mechanics force field of MMFF94 for optimization and CHARMM27 for MD simulation. In addition, in-house scripts written in Matlab were used to control fragments connection and automation of the tools.

N-substituted tetrahydro-beta-carboline as mu-opioid receptors ligands: in silico study; molecular docking, ADMET and molecular dynamics approach.

Manipulating intracellular signals by interaction with transmembranal G-protein-coupled receptors (GPCRs) is the way of action of more than 30% of available medicines. Designing molecules against GPCRs is most challenging due to their flexible binding orthosteric and allosteric pockets, a property that lead to different mode and extent of activation of intracellular mediators. Here, in the current study we aimed to design N-substituted tetrahydro-beta-carbolines (THßC's) targeting Mu Opioid Receptors (MORs). We performed ligand docking study for reference and designed compounds against active and inactive states of MOR, as well as the active state bound to intracellular mediator of Gi. The reference compounds include 40 known agonists and antagonists, while the designed compounds include 25,227 N-substituted THßC analogues. Out of the designed compounds, 15 compounds were comparatively having better extra precision (XP) Gscore and were analyzed for absorption, distribution, metabolism, and excretion-toxicity (ADMET) properties, drug-likness, and molecular dynamic (MD) simulation. The results showed that N-substituted tetrahydro-beta-carbolines with and without C6-methoxy group substitutions (THBC/6MTHBC) analogues of A1/B1 and A9/B9 have relatively acceptable affinity and within pocket-stability toward MOR compared to the reference compounds of morphine (agonist) and naloxone (antagonist). Moreover, the designed analogues interact with key residue within the binding pocket of Asp 147 that is reported to be involved in receptor activation. In conclusion, the designed THBC analogues represent a good starting point for designing opioid receptor ligands other than morphinan scaffold, that have good synthetic accessibility which promotes feasible structural manipulation to tailor pharmacological effects with minimal side effects. Workflow rational in the discovery of potential Mu Opioid Receptor ligands.

Late-onset multiple venous malformations confined to the upper limb: link to somatic MAP3K3 mutations.

Venous (cavernous) malformations are commonly seen in the upper limb. Almost all venous malformations are congenital. They may be sporadic, familial, or syndromic. Late-onset, multiple venous malformations confined to the upper limb are rare. Lesions present after puberty. All previously reported cases were located subcutaneously and were small in size. The condition is non-hereditary and non-syndromic. We present a unique series of eight patients with this rare condition. Unique features included the presence of large malformations (up to 20 cm in diameter) and the presence of subfascial lesions causing nerve compression. Surgical excision was curative. Mutational analysis in one patient identified a novel somatic MAP3K3 gene mutation (c.1723T > C, p.Tyr 575 His) in the affected veins. The encoded MAP3K3 protein is known to accelerate the RAS pathway of cellular proliferation.Level of evidence: IV.

Molecular Basis of Modulating Adenosine Receptors Activities.

Modulating cellular processes through extracellular chemical stimuli is medicinally an attractive approach to control disease conditions. GPCRs are the most important group of transmembranal receptors that produce different patterns of activations using intracellular mediators (such as G-proteins and Beta-arrestins). Adenosine receptors (ARs) belong to GPCR class and are divided into A1AR, A2AAR, A2BAR and A3AR. ARs control different physiological activities thus considered valuable target to control neural, heart, inflammatory and other metabolic disorders. Targeting ARs using small molecules essentially works by binding orthosteric and/or allosteric sites of the receptors. Although targeting orthosteric site is considered typical to modulate receptor activity, allosteric sites provide better subtype selectivity, saturable modulation of activity and variable activation patterns. Each receptor exists in dynamical equilibrium between conformational ensembles. The equilibrium is affected by receptor interaction with other molecules. Changing the population of conformational ensembles of the receptor is the method by which orthosteric, allosteric and other cellular components control receptor signaling. Herein, the interactions of ARs with orthosteric, allosteric ligands as well as intracellular mediators are described. A quinary interaction model for the receptor is proposed and energy wells for major conformational ensembles are retrieved.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery.

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.

Technique of Split Flexor Carpi Ulnaris Opponensplasty.

The classic donor motor units for opponensplasty are the flexor digitorum superficialis, the extensor indicis proprius, the palmaris longus, and the abductor digiti minimi. Occasionally, all classic donor motor units are not available for the opponensplasty; a review of the literature revealed that the flexor carpi ulnaris opponensplasty has not been previously described. The surgical technique of the split flexor carpi ulnaris opponensplasty is described in the current paper along with a clinical example. The result in our patient was satisfactory with the ability to oppose the thumb tip to reach the tip of the ring finger with the wrist in neutral position.

The postauricular fasciocutaneous flap with an adipofascial extension: A case report.

INTRODUCTION: A complex defect on the anterior surface of the ear requires flap cover; such as the postauricular skin flap. The postauricular skin flap has never been used with an adipofascial extension. PRESENTATION OF CASE: A 5-year old boy was involved in a car accident resulting in an exposed cartilage of the upper part of the right ear. The defect was covered with a post-auricular fasciocutaneous flap with an adipofascial extension. The adipofascial part of the flap was covered with a skin graft. DISCUSSION: The adipofascial extension serves two purposes: Firstly, it allows easier primary closure of the donor site. Secondly, it is less bulky and hence it does not observe the definition of the ear cartilage. CONCLUSION: Our case is the first case reported in literature using the post-auricular fasciocutaneous flap with an adipofascial extension.

Assembly of ligands interaction models for glutathione-S-transferases from Plasmodium falciparum, human and mouse using enzyme kinetics and molecular docking.

BACKGROUND: Glutathione-s-transferases (GSTs) are enzymes that principally catalyze the conjugation of electrophilic compounds to the endogenous nucleophilic glutathione substrate, besides, they have other non-catalytic functions. The Plasmodium falciparum genome encodes a single isoform of GST (PfGST) which is involved in buffering the toxic heme, thus considered a potential anti-malarial target. In mammals several classes of GSTs are available, each of various isoforms. The human (human GST Pi-1 or hGSTP1) and mouse (murine GST Mu-1 or mGSTM1) GST isoforms control cellular apoptosis by interaction with signaling proteins, thus considered as potential anti-cancer targets. In the course of GSTs inhibitors development, the models of ligands interactions with GSTs are used to guide rational molecular modification. In the absence of X-ray crystallographic data, enzyme kinetics and molecular docking experiments can aid in addressing ligands binding modes to the enzymes. METHODS: Kinetic studies were used to investigate the interactions between the three GSTs and each of glutathione, 1-chloro-2,4-dinitrobenzene, cibacron blue, ethacrynic acid, S-hexyl glutathione, hemin and protoporphyrin IX. Since hemin displacement is intended for PfGST inhibitors, the interactions between hemin and other ligands at PfGST binding sites were studied kinetically. Computationally determined binding modes and energies were interlinked with the kinetic results to resolve enzymes-ligands interaction models at atomic level. RESULTS: The results showed that hemin and cibacron blue have different binding modes in the three GSTs. Hemin has two binding sites (A and B) with two binding modes at site-A depending on presence of GSH. None of the ligands were able to compete hemin binding to PfGST except ethacrynic acid. Besides bind differently in GSTs, the isolated anthraquinone moiety of cibacron blue is not maintaining sufficient interactions with GSTs to be used as a lead. Similarly, the ethacrynic acid uses water bridges to mediate interactions with GSTs and at least the conjugated form of EA is the true hemin inhibitor, thus EA may not be a suitable lead. CONCLUSIONS: Glutathione analogues with bulky substitution at thiol of cysteine moiety or at γ-amino group of γ-glutamine moiety may be the most suitable to provide GST inhibitors with hemin competition.

Use of the Volar Plate of the Distal Interphalangeal Joint as a Distally Based Flap in Flexor Tendon Surgery.

The usual treatment for flexor digitorum profundus (FDP) avulsions as well as FDP lacerations in the distal part of zone I is tendon reinsertion into bone. Although there are several different techniques of FDP tendon reinsertion into bone, they are generally complex and have a weak tensile strength. A technique for treating these injuries is to use the volar plate of the distal interphalangeal joint as a distally based flap for tendon repair. The current communication discusses the technique and its potential complications. Initial clinical experience is encouraging and the volar plate flap technique may take its place in flexor tendon surgery.

Myofibroblast expression in skin wounds is enhanced by collagen III suppression.

Generally speaking, the excessive expression of myofibroblasts is associated with excessive collagen production. One exception is seen in patients and animal models of Ehlers-Danlos syndrome type IV in which the COL3A1 gene mutation results in reduced collagen III but with concurrent increased myofibroblast expression. This paradox has not been examined with the use of external drugs/modalities to prevent hypertrophic scars. In this paper, we injected the rabbit ear wound model of hypertrophic scarring with two doses of a protein called nAG, which is known to reduce collagen expression and to suppress hypertrophic scarring in that animal model. The higher nAG dose was associated with significantly less collagen III expression and concurrent higher degree of myofibroblast expression. We concluded that collagen III content of the extracellular matrix may have a direct or an indirect effect on myofibroblast differentiation. However, further research is required to investigate the pathogenesis of this paradoxical phenomenon.

Docking of sialic acid analogues against influenza A hemagglutinin: a correlational study between experimentally measured and computationally estimated affinities.

A molecular docking tool of AutoDock3.05 was evaluated for its ability to reproduce experimentally determined affinities of various sialic acid analogues toward hemagglutinin of influenza A virus. With the exception of those with a C6-modified glycerol side chain, the experimental binding affinities of most sialic acid analogues (C2, C4 and C5-substituted) determined by viral hemadsorption inhibition assay, hemagglutination inhibition assay and nuclear magnetic resonance correlated well with the computationally estimated free energy of binding. Sialic acid analogues with modified glycerol side chains showed only poor correlation between the experimentally determined hemagglutinin inhibitor affinities and AutoDock3.05 scores, suggesting high mobility of the glutamic acid side chain at the glycerol binding pocket, which is difficult to simulate using a flexi-rigid molecular docking approach. In conclusion, except for some glycerol-substituted sialic acid analogues, the results showed the effectiveness of AutoDock3.05 searching and scoring functions in estimating affinities of sialic acid analogues toward influenza A hemagglutinin, making it a reliable tool for screening a database of virtually designed sialic acid analogues for hemagglutinin inhibitors.

Site-directed fragment-based generation of virtual sialic acid databases against influenza A hemagglutinin.

In this study fragment-based drug design is combined with molecular docking simulation technique, to design databases of virtual sialic acid (SA) analogues with new substitutions at C2, C5 and C6 positions of SA scaffold. Using spaces occupied by C2, C5 and C6 natural moieties of SA when bound to hemagglutinin (HA) crystallographic structure, new fragments that are commercially available were docked independently in all the pockets. The oriented fragments were then connected to the SA scaffold with or without incorporation of linker molecules. The completed analogues were docked to the whole SA binding site to estimate their binding conformations and affinities, generating three databases of HA-bound SA analogues. Selected new analogues showed higher estimated affinities than the natural SA when tested against H3N2, H5N1 and H1N1 subtypes of influenza A. An improvement in the binding energies indicates that fragment-based drug design when combined with molecular docking simulation is capable to produce virtual analogues that can become lead compound candidates for anti-flu drug discovery program.

An obstetric brachial plexus data sheet.

BACKGROUND: Several reputed obstetric brachial plexus clinics use their own protocols and indications for surgery. This study is to present and explain the obstetric brachial plexus data sheet used at our institution. METHODS: The data sheet is composed of 5 main parts: (1) the basic database which includes the name, age, type and side of palsy, maternal history, birth history and other complications of the traumatic delivery; (2) motor assessment of the limb; (3) preoperative investigations; (4) description of intraoperative brachial plexus findings and type of nerve procedure performed; and (5) secondary surgery to the shoulder, elbow, forearm, wrist and hand. RESULTS: The data sheet was found useful in documenting the assessment and events in infants and older children. CONCLUSION: An obstetric brachial plexus data sheet is presented and it may be modified and used by other centers.

On the neglected entity of unilateral gynecomastia.

Although there are many articles in the literature on the etiology, classification, and management of gynecomastia, the entity of unilateral gynecomastia has not received much attention. In this article, 15 consecutive males (seen over a 10-year period) with unilateral gynecomastia were retrospectively reviewed. The study showed the unique presentation in this group of patients. One third of the patients (n = 5) had "cancer phobia" and were worried either because of the presence of a mass (n = 2) or because of the unilaterality of their disease (n = 3). The study also showed the predominance of true (glandular) gynecomastia, and this has also been observed in other cases of unilateral involvement in the literature. All patients underwent preoperative mammography. Mammographic findings were consistent with gynecomastia in all patients, including the 2 patients with concurrent breast masses. All patients underwent subcutaneous mastectomy, and histologic examination confirmed the diagnosis. Finally, the literature on unilateral gynecomastia was reviewed.

Surgical correction of primary cutis vertices gyrata.

Primary cutis vertices gyrata is a rare condition of the scalp characterized by the formation of furrows and folds resembling the convolutions of the brain. A review of the English literature did not reveal any surgically treated cases. The authors report three cases treated by simple excision of the deepest furrows with a satisfactory result.