45 research outputs found
Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function
Indinavir (CrivaxanÂź) is a potent inhibitor of the HIV (human immunodeficiency virus) protease. This enzyme has an important role in viral
replication and is considered to be very attractive target for new antiretroviral drugs. However, it becomes less effective due to highly resistant
new viral strains of HIV, which have multiple mutations in their proteases. For this reason, we used a lead expansion method to create a new set
of compounds with a new mode of action to protease binding site. 1300 compounds chemically diverse from the initial hit were generated and
screened to determine their ability to interact with protease and establish their QSAR properties. Further computational analyses revealed one
unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed
in this report
Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors
CITATION: Isaacs, Darren et al. 2020. Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors. Viruses, 12(9):936, doi:10.3390/v12090936.The original publication is available at: https://www.mdpi.comENGLISH ABSTRACT: The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naĂŻve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance.Publisher's versio
Structural comparison of diverse HIV-1 subtypes using molecular modelling and docking analyses of integrase inhibitors
The process of viral integration into the host genome is an essential step of the HIV-1 life cycle. The viral integrase (IN) enzyme catalyzes integration. IN is an ideal therapeutic enzyme targeted by several drugs; raltegravir (RAL), elvitegravir (EVG), dolutegravir (DTG), and bictegravir (BIC) having been approved by the USA Food and Drug Administration (FDA). Due to high HIV-1 diversity, it is not well understood how specific naturally occurring polymorphisms (NOPs) in IN may affect the structure/function and binding affinity of integrase strand transfer inhibitors (INSTIs). We applied computational methods of molecular modelling and docking to analyze the effect of NOPs on the full-length IN structure and INSTI binding. We identified 13 NOPs within the Cameroonian-derived CRF02_AG IN sequences and further identified 17 NOPs within HIV-1C South African sequences. The NOPs in the IN structures did not show any differences in INSTI binding affinity. However, linear regression analysis revealed a positive correlation between the Ki and EC50 values for DTG and BIC as strong inhibitors of HIV-1 IN subtypes. All INSTIs are clinically effective against diverse HIV-1 strains from INSTI treatment-naĂŻve populations. This study supports the use of second-generation INSTIs such as DTG and BIC as part of first-line combination antiretroviral therapy (cART) regimens, due to a stronger genetic barrier to the emergence of drug resistance
Platelet glycoprotein VI promotes metastasis through interaction with cancer cell-derived Galectin-3
Ionization States, Cellular Toxicity and Molecular Modeling Studies of Midazolam Complexed with Trimethyl-ÎČ-Cyclodextrin
We investigated the ionization profiles for open-ring (OR) and closed-ring (CR) forms of midazolam and drug-binding modes with heptakis-(2,3,6-tri-O-methyl)-ÎČ-cyclodextrin (trimethyl-ÎČ-cyclodextrin; TRIMEB) using molecular modeling techniques and quantum mechanics methods. The results indicated that the total net charges for different molecular forms of midazolam tend to be cationic for OR and neutral for CR at physiological pH levels. The thermodynamic calculations demonstrated that CR is less water-soluble than OR, mainly due to the maximal solvation energy ((Delta G_{solv}^{CR}) = â9.98 kcal·mol(^{â1})), which has a minimal (Delta G_{solv}^{OR}) of â67.01 kcal·mol(^{â1}). A cell viability assay did not detect any signs of TRIMEB and OR/CR-TRIMEB complex toxicity on the cEND cells after 24 h of incubation in either Dulbecco\u27s Modified Eagles Medium or in heat-inactivated human serum. The molecular docking studies identified the more flexible OR form of midazolam as being a better binder to TRIMEB with the fluorophenyl ring introduced inside the amphiphilic cavity of the host molecule. The OR binding affinity was confirmed by a minimal Gibbs free energy of binding ((Delta G_{bind})) value of â5.57 ± 0.02 kcal·mol(^{â1}), an equilibrium binding constant ((K_{b})) of 79.89 ± 2.706 ÎŒM, and a ligand efficiency index ((LE_{lig})) of â0.21 ± 0.001. Our current data suggest that in order to improve the clinical applications of midazolam via its complexation with trimethyl-ÎČ-cyclodextrin to increase drug\u27s overall aqueous solubility, it is important to concern the different forms and ionization states of this anesthetic. All mean values are indicated with their standard deviations
Simulationen und Interaktionen viraler Proteine sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen
Molecular modelling and simulation are powerful methods in providing important in-formation on different biological systems to elucidate their structural and functional proper-ties, which cannot be determined in experiment. These methods are applied to analyse versa-tile biological systems: lipid membrane bilayers stabilized by an intercalated single wall carbon nanotube and retroviral proteins such as HIV protease and integrase. HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. Previously it was shown that NLSs bind to the cell transport machinery e.g. proteins of nuclear pore complex such as transportins. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2. These results were discussed in comparison to other retroviral species such as foamy viruses to better understand this specific and efficient retroviral trafficking route. The retroviral nuclear import was next analyzed in experiments regarding the retroviral ability to infect nondividing cells. To accomplish the gene transfer task successfully, ret-roviruses must efficiently transduce different cell cultures at different phases of cell cycle. However, promising and safe foamy viral vectors used for gene transfer are unable to effi-ciently infect quiescent cells. This drawback was due to their inability to create a preintegra-tion complex (PIC) for nuclear import of retroviral DNA. On the contrary, the lentiviral vec-tors are not dependant on cell cycle. In the course of reverse transcription the polypurine tract (PPT) is believed to be crucial for PIC formation. In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to effi-ciently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains. Many attempts have been made recently to search for the potential molecules as pos-sible drug candidates to treat HIV infection for over decades now. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthe-sized in a laboratory. Most notably, one could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. Such structure-based drug design strategies have the potential to save off years and millions of dollars compared to a more traditional trial-and-error drug development process. After the crystal structure of the HIV-encoded protease enzyme had been elucidated, computer-aided drug design played a pivotal role in the development of new compounds that inhibit this enzyme which is responsible for HIV maturation and infectivity. Promising repre-sentatives of these compounds have recently found their way to patients. Protease inhibitors show a powerful sustained suppression of HIV-1 replication, especially when used in combi-nation therapy regimens. However, these drugs are becoming less effective to more resistant HIV strains due to multiple mutations in the retroviral proteases. In computational drug design I used molecular modelling methods such as lead ex-pansion algorithm (TriposÂź) to create a virtual library of compounds with different binding affinities to protease binding site. In addition, I heavily applied computer assisted combinato-rial chemistry approaches to design and optimize virtual libraries of protease inhibitors and performed in silico screening and pharmacophore-similarity scoring of these drug candidates. Further computational analyses revealed one unique compound with different protease bind-ing ability from the initial hit and its role for possible new class of protease inhibitors is dis-cussed (Shityakov and Dandekar, 2009). A number of atomistic models were developed to elucidate the nanotube behaviour in lipid bilayers. However, none of them provided useful information for CNT effect upon the lipid membrane bilayer for implementing all-atom models that will allow us to calculate the deviations of lipid molecules from CNT with atomistic precision. Unfortunately, the direct experimental investigation of nanotube behaviour in lipid bilayer remains quite a tricky prob-lem opening the door before the molecular simulation techniques. In this regard, more de-tailed multi-scale simulations are needed to clearly understand the stabilization characteristics of CNTs in hydrophobic environment. The phenomenon of an intercalated single-wall carbon nanotube in the center of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid mem-branes. The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). On the other hand, different lipid membranes may have dissimilarities due to the differing abilities to create a bridge formation between the adherent lipid molecules. The results derived from this thesis will help to develop stable nanobiocom-posites for construction of novel biomaterials and delivery of various biomolecules for medi-cine and biology.Molekulare Modellierung und Simulationen sind leistungsstarke Methoden, um wich-tige Informationen von verschiedenen biologischen Systemen, welche nicht durch Experi-mente erschlossen werden können, darzustellen, und deren strukturelle und funktionelle Ei-genschaften aufzuklĂ€ren. Diese Arbeit untersucht in Simulationen Interaktionen viraler Proteinen sowie von Kohlenstoffenanoröhren mit Membranen und Proteinen. Die HIV-1 Integrase besitzt Kernlokalisierungssignale (ânuclear localization signals [NLS]â), welche eine entscheidende Rolle beim Import des viralen PrĂ€integrationskomplexes (âpreintegration complex [PIC]â) in den Zellkern spielen. Die Ausbildung des PIC und sein Import in den Zellkern sind im Detail noch nicht bekannt. Es wurde bereits gezeigt, dass die NLS an MolekĂŒle des Zelltransportsystems binden, wie z.B. an Transportinkernporen. Im Rahmen meiner Arbeit untersuchte ich die Interaktionen der viralen HIV-1 Integrase mit Proteinen der Kernporen wie dem Transportin-SR2 Protein (Shityakov et al., 2010). Hierbei wurden die möglichen Interaktionen des Transportin-SR2 Protein mit der HIV-1-Integrase und die Bedeutung dieser Interaktionen mit dem Import in den Kern aufgezeigt. Zudem wur-den die Interaktionen der SchlĂŒsseldomĂ€nen und die Ausbildung von WasserstoffbrĂŒcken-bindungen im dem Transportin-SR2 Protein untersucht. Die Ergebnisse wurden mit Protein-komplexen andere retroviralen Spezies, wie z.B. dem humanen Spumaretrovirus (âhuman foamy virus [HFV]â), verglichen, um diesen spezifischen und sehr effizienten retroviralen Transportweg in die Wirtszelle zu entschlĂŒsseln. Der experimentelle Teil dieser Arbeit beschĂ€ftigte sich damit, den retroviralen Kern-import zu untersuchen, um die FĂ€higkeit des Retrovirus, nicht teilende Zellen zu infizieren, besser zu verstehen verstanden wird. Um dies zu bewerkstelligen, mĂŒssen Retroviren Zellkul-turen in verschiedenen Stadien des Zellzyklus effizient transduzieren. Vielversprechende und sichere- HFV- Vektoren, welche in der Gentherapie eingesetzt werden könnten, sind nicht in der Lage, diese Effizienz bei ruhenden Zellen zu gewĂ€hrleisten. Dies rĂŒhrte daher, dass diese nicht in der Lage waren, einen PIC fĂŒr den Transport der retroviralen DNA auszubilden. Lentivirale Vektoren sind dagegen nicht auf einen bestimmten Zellzyklus angewiesen. FĂŒr die reverse Transkription ist der Polypurinteil (âpolypurine tract [PPT]â) essentiell fĂŒr die Ausbildung der PIC. In dieser Doktorarbeit vergleiche ich die Transduktionsfrequenz von PPT-modifizierten HFV-Vektoren mit denen von lentiviralen Vektoren in nichtteilenden und tei-lenden Lungenkarzinomepithelzellen. Hierbei wurden Methoden wie Klonierung, Transfektion, und Transduktion (wie auch weitere Methoden) angewendet. Im Gegensatz zu lentiviralen Vektoren konnten HFV-Vektoren sich nicht teilende Zellen in meinen Versuchen nicht effizient transduzieren (Shityakov und Rethwiln, unveröffentlicht). Trotz der Befunde, dass HFV-Vektoren sichere und effiziente Alternativen zu lentiviralen Vektoren darstellen, bestehen immer noch groĂe EinschrĂ€nkungen, diese HFV-basierten, retroviralen Vektoren fĂŒr Gentherapien bei ruhenden Zellen einzusetzen. Viele Versuche wurden unternommen, um mögliche, vielversprechende MolekĂŒle, welche als Wirkstoffe fĂŒr eine HIV-Therapie eingesetzt werden könnten, zu finden. Diese MolekĂŒle können aus chemischen Substanzbibliotheken bezogen werden oder am Computer in silico entworfen und dann synthetisiert werden. Digitalisierte Strukturen können als Refe-renzen benutzt werden, um besser herauszufinden, wie diese MolekĂŒle Typen diverse Enzy-me blokieren könnten. Strukturbasiertes Wirkstoffdesign hat das Potential, viele Jahre und Geld an Entwicklungskosten einzusparen. Nachdem die Kristallstruktur der HIV-kodierten Proteasen aufgeklĂ€rt war, spielte das computergestĂŒtzte Wirkstoffdesign eine zentrale Rolle bei der Entwicklung neuer Wirkstoffe gegen die Protease. Vielversprechende Vertreter dieser Wirkstoffklasse werden seit kurzem nun auch fĂŒr die Behandlung von Patienten eingesetzt. Proteaseinhibitoren zeigen eine wir-kungsvolle und langanhaltende Inhibition der HIV-1-Replikation; besonders dann, wenn sie in Kombinationstherapien eingesetzt werden. Aber diese Wirkstoffe werden immer weniger effektiv, je resistenter die HIV-StĂ€mme durch Mutationen in den retroviralen Proteasen wer-den. Im Rahmen meiner Arbeit mit computergestĂŒtztem Wirkstoffdesign nutzte ich Model-lierungsmethoden wie den âlead expansion algorithmâ (TriposÂź) um virtuelle Wirkstoffbibli-otheken mit verschiedenen AffinitĂ€ten zur Proteasebindungsstelle zu erstellen. ZusĂ€tzlich wandte ich Verfahren der computergestĂŒtzten, kombinatorischen Chemie an, um virtuelle Bibliotheken von Proteaseinhibitoren zu designen, und zu verbessern. Parallel dazu wurde eine in silico Selektion sowie eine Einteilung nach PharmakophorĂ€hnlichkeiten fĂŒr diese Kandidaten vorgenommen. WeiterfĂŒhrende computergestĂŒtzte Analysen förderten einen ein-zigartigen Wirkstoff zu Tage, welcher neuartige Proteasebindungseigenschaften aufweist, und dessen Rolle fĂŒr eine potentiell neuartige Klasse von Proteaseinhibitoren schon beschrieben wurde (Shityakov und Dandekar, 2009). Eine Reihe von Modellen mit atomarer Auflösung wurden bereits entwickelt, um das Verhalten von Nanoröhren in Lipid-Doppelschichten aufzuklĂ€ren. Die Auswirkungen auf die molekular Dynamik einer einschichtigen Karbonnanoröhre, welche in das Zentrum einer Lipid-Doppelschicht eingefĂŒgt wurde, wurden intensiv studiert und analysiert. Die Normalabweichung und Fluktuationen wurden berechnet, um eine Aussage ĂŒber die StabilitĂ€t der Lipid-Doppelschichten treffen zu können. Die Ergebnisse weisen darauf hin, dass eine eingefĂŒgte Karbonnanoröhre die Freiheit fĂŒr KonformationsĂ€nderungen bei nahegelegenen Lipiden einschrĂ€nkt und dadurch einen Einfluss auf die MembranstabilitĂ€t hat (Shityakov und Dandekar, 2011). Es kann aber auĂer-dem sein, dass verschiedene Lipid-Doppelschichten Unterschiede in ihrer FĂ€higkeit, BrĂŒcken zwischen benachbarten Lipiden auszubilden, aufweisen. Viren und Karbonnanoröhren werden damit in verschiedenen dynamischen Simulati-onen untersucht, um mehr ĂŒber ihre Interaktionen mit Proteinen und Membranen zu erfahren
α-Cyclodextrin dimer complexes of dopamine and levodopa derivatives to assess drug delivery to the central nervous system: ADME and molecular docking studies
Rational drug design of Axl tyrosine kinase type I inhibitors as promising candidates against cancer
The high level of Axl tyrosine kinase expression in various cancer cell lines makes it an attractive target for the development of anti-cancer drugs. In this study, we carried out several sets of in silico screening for the ATP-competitive Axl kinase inhibitors based on different molecular docking protocols. The best drug-like candidates were identified, after parental structure modifications, by their highest affinity to the target protein. We found that our newly designed compound R5, a derivative of the R428 patented analog, is the most promising inhibitor of the Axl kinase according to the three molecular docking algorithms applied in the study. The molecular docking results are in agreement with the molecular dynamics simulations using the MM-PBSA/GBSA implicit solvation models, which confirm the high affinity of R5 toward the protein receptor. Additionally, the selectivity test against other kinases also reveals a high affinity of R5 toward ABL1 and Tyro3 kinases, emphasizing its promising potential for the treatment of malignant tumors
Pharmacokinetic Delivery and Metabolizing Rate of Nicardipine Incorporated in Hydrophilic and Hydrophobic Cyclodextrins Using Two-Compartment Mathematical Model
The dispersion routes of cyclodextrin complexes with nicardipine (NC), such as hydrophilic hydroxypropyl--cyclodextrin (NC/HPCD) and hydrophobic triacetyl--cyclodextrin (NC/TACD), through the body for controlled drug delivery and sustained release have been examined. The two-compartment pharmacokinetic model described the mechanisms of how the human body handles with ingestion of NC-cyclodextrin complexes in gastrointestinal tract (GI), distribution in plasma, and their metabolism in the liver. The model showed that drug bioavailability was significantly improved after oral administration of cyclodextrin complexes. The mathematical significance of this study to predict nicardipine delivery using pharmacokinetic two-compartment mathematical model with linear ordinary differential equations (ODE) approach represents a valuable tool to emphasize its effectiveness and metabolizing rate and diminish the side effects
Evaluation and Prediction of the HIV-1 Central Polypurine Tract Influence on Foamy Viral Vectors to Transduce Dividing and Growth-Arrested Cells
Retroviral vectors are potent tools for gene delivery and various biomedical applications. To accomplish a gene transfer task successfully, retroviral vectors must effectively transduce diverse cell cultures at different phases of a cell cycle. However, very promising retroviral vectors based on the foamy viral (FV) backbone lack the capacity to efficiently transduce quiescent cells. It is hypothesized that this phenomenon might be explained as the inability of foamy viruses to form a pre-integration complex (PIC) with nuclear import activity in growth-arrested cells, which is the characteristic for lentiviruses (HIV-1). In this process, the HIV-1 central polypurine tract (cPPT) serves as a primer for plus-strand synthesis to produce a âflapâ element and is believed to be crucial for the subsequent double-stranded cDNA formation of all retroviral RNA genomes. In this study, the effects of the lentiviral cPPT element on the FV transduction potential in dividing and growth-arrested (G1/S phase) adenocarcinomic human alveolar basal epithelial (A549) cells are investigated by experimental and theoretical methods. The results indicated that the HIV-1 cPPT element in a foamy viral vector background will lead to a significant reduction of the FV transduction and viral titre in growth-arrested cells due to the absence of PICs with nuclear import activity