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Abstract

Next-generation molecular force fields deliver accurate descriptions of non-covalent interactions by employing more elaborate functional forms than their predecessors. Much work has been dedicated to improving the description of the electrostatic potential (ESP) generated by these force fields. A common approach to improving the ESP is by augmenting the point charges on each center with higher-order multipole moments. The resulting anisotropy greatly improves the directionality of the non-covalent bonding, with a concomitant increase in computational cost. In this work, we develop an efficient strategy for enumerating multipole interactions, by casting an efficient spherical harmonic based approach within a particle mesh Ewald (PME) framework. Although the derivation involves lengthy algebra, the final expressions are relatively compact, yielding an approach that can efficiently handle both finite and periodic systems without imposing any approximations beyond PME. Forces and torques are readily obtained, making our method well suited to modern molecular dynamics simulations.An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald. Pathogenic microbes can recruit to their cell surface human proteins that are components of important proteolytic cascades involved in coagulation, fibrinolysis and innate immune response. Once located at the bacterial or fungal surface, such deployed proteins might be utilized by pathogens to facilitate invasion and dissemination within the host organism by interfering with functionality of these systems or by exploiting specific activity of the bound enzymes. After confirming ability of the fungal surface-exposed proteins to bind HPG and HK, four of them – two agglutinin-like sequence (Als) proteins CPAR2_404780 and CPAR2_404800, a heat shock protein Ssa2 and a moonlighting protein 6-phosphogluconate dehydrogenase 1 – were purified using ion-exchange chromatography, gel filtration and chromatofocusing. Then, their affinities to HPG and HK were characterized with surface plasmon resonance measurements. The determined dissociation constants for the investigated protein-protein complexes were within a 10-7 M order for the HPG binding and in a range of 10-8-10-9 M for the HK binding. Detailed characterization of adsorption of these two important plasma proteins on the fungal cell surface may help to increase our understanding of molecular mechanisms of C. parapsilosis-dependent candidiasis. Pathogenic microbes can recruit to their cell surface human proteins that are components of important proteolytic cascades involved in coagulation, fibrinolysis and innate immune response. Once located at the bacterial or fungal surface, such deployed proteins might be utilized by pathogens to facilitate invasion and dissemination within the host organism by interfering with functionality of these systems or by exploiting specific activity of the bound enzymes. Aim of the study presented here was to characterize this phenomenon in Candida parapsilosis (Ashford) Langeron et Talice – an important causative agent of systemic fungal infections (candidiases and candidemias) in humans. We have investigated the interactions of fungal surface-exposed proteins with plasminogen (HPG) and high-molecular-mass kininogen (HK) – the crucial components of human fibrinolytic system and proinflammatory/procoagulant contact-activated kinin-forming system, respectively. After confirming ability of the fungal surface-exposed proteins to bind HPG and HK, four of them – two agglutinin-like sequence (Als) proteins CPAR2_404780 and CPAR2_404800, a heat shock protein Ssa2 and a moonlighting protein 6-phosphogluconate dehydrogenase 1 – were purified using ion-exchange chromatography, gel filtration and chromatofocusing. Then, their affinities to HPG and HK were characterized with surface plasmon resonance measurements. The determined dissociation constants for the investigated protein-protein complexes were within a 10-7 M order for the HPG binding and in a range of 10-8-10-9 M for the HK binding. Detailed characterization of adsorption of these two important plasma proteins on the fungal cell surface may help to increase our understanding of molecular mechanisms of C. parapsilosis-dependent candidiasis.Abstract: Candida albicans is one of the most common opportunistic human fungal pathogens. In healthy human populations, it is a member of the normal flora of the skin, genital, and intestinal mucosa. However, C. albicansas well as other Candida species (e.g., C. parapsilosis or C. krusei) may lead to morbidity and mortality in immunocompromised patients as a consequence of fungal overgrowth and severe cutaneous or systemic infections. For the treatment of invasive candidiasis, amphotericin B-based preparations, azoles, and echinocandins are used. In the therapy of mucocutaneous infections (e.g., vaginal infections), azoles are the dominant agents. The synthetic peptides TKCFQWQRNMRKVRGPPVSCIKR Lfpep and FFSASCVPGADKGQFPNLCRLCAGTGENKCA kaliocin-1 include the sequences from positions 18 to 40 and 153 to 183 of human lactoferrin, respectively. In this research we will give the lead in a new drug discovery paradigm that focuses on mechanisms of action. Furthermore, the technologies developed in this project will offer new pharmaceutical chemico-scaffolds to facilitate basic scientific research. Within the next three years, Biogenea SA will contribute proprietary resources to take the new drug compounds through clinical trials and ultimately to market using an efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald Binding of human plasminogen and high-molecular-mass kininogen by cell surface-exposed proteins of Candida parapsilosis.

Keywords

Ultimate; target-ligand based approaches;experimental; predicted binding affinity; matrices; Chemogenomics-Driven; NCR, Lfpep, Brevinin-1Sa;kaliocin-1; peptidomimetic; Drug Discovery; Neo-agent; Candida albicans; CXG motif; signatures; efficient algorithm; multipole energies; derivatives; spherical harmonics; extensions; particle mesh Ewald;

Article Type

Research Article – Abstract

Publication history

Received: Sep 20, 2017
Accepted: Sep 25, 2017
Published: Oct 01, 2017

Citation

Grigoriadis Ioannis, Grigoriadis George, Grigoriadis Nikolaos, George Galazios (2017) Ultimate target-ligand based approaches using predicted binding affinity matrices as a Chemogenomics-Driven NCR, Lfpep, Brevinin-1Sa and kaliocin-1 peptidomimetic Drug Discovery Neo-agent against Candida albicans antimicrobial CXG motif signatures.

Authors Info

Grigoriadis Nikolaos
Department of IT Computer Aided Personalized Myoncotherapy, Cartigenea-Cardiogenea, Neurogenea-Cellgenea, Cordigenea-HyperoligandorolTM,
Biogenea Pharmaceuticals Ltd,
Thessaloniki, Greece;

Grigoriadis Ioannis
Department of Computer Drug Discovery Science, BiogenetoligandorolTM,
Biogenea Pharmaceuticals Ltd,
Thessaloniki, Greece;

Grigoriadis George
Department of Stem Cell Bank and ViroGeneaTM,
Biogenea Pharmaceuticals Ltd,
Thessaloniki, Greece;

George Galazios
Professor of Obstetrics and Gynecology,
Democritus University of Thrace,
Komotini, Greece;

E-mail: biogeneadrug@gmail.com

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