Use of Structure-And Ligand-Based Drug Design Tools for the Discovery of Small Molecule Inhibitors of Cysteine Proteases for the Treatment of Malaria and Sars Infection

A wide array of molecular modeling tools were utilized to design and develop inhibitors against cysteine protease of P. Falciparum Malaria and Severe Acute Respiratory Syndrome (SARS). A number of potent inhibitors were developed against cysteine protease and hemoglobinase of P. falciparum , referred as Falcipains (FPs), by the structure-based virtual screening of the focused libraries enriched in soft-electrophiles containing compounds. Twenty one diverse, non-peptidic, low micromolar hits were identified. A combined data mining and combinatorial library synthesis approach was performed to discover analogs of virtual screening hits and establish the structure-activity relationships (SAR). However, the resulting SAR of the identified hits was unusually steep in some cases and could not be explained by a traditional analysis of the interactions (electrostatics, van der Waals or H-bond). To gain insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domain of FP-2 and FP-3 was performed that explained some of the complex trends in the SAR. Furthermore, the moderate potency of a subset of FP-2 hits was elucidated using quantum mechanics calculations that shoreduced reactivity of the electrophilic center of these hits. In addition, solvent thermodynamics and reactivity analysis also helped to elucidate the complex trends in SAR of peptidomimetic inhibitors of FP-2 and FP-3 synthesized in our laboratory. Multi nanosecond explicit solvent molecular dynamics simulations were carried out using the docking poses of the known inhibitors in the binding site of SARS-3CLpro, a cysteine protease important for replication of SARS virus, to study the overall stability of the binding site interactions as well as identify important changes in the interaction profile that were not apparent from the docking study. Analysis of the simulation studies led to the identification of certain protein-ligand interaction patterns which would be useful in further structure based design efforts against cysteine protease (3CLpro) of SARS

Proteases in Malaria Parasites - A Phylogenomic Perspective

Malaria continues to be one of the most devastating global health problems due to the high morbidity and mortality it causes in endemic regions. The search for new antimalarial targets is of high priority because of the increasing prevalence of drug resistance in malaria parasites. Malarial proteases constitute a class of promising therapeutic targets as they play important roles in the parasite life cycle and it is possible to design and screen for specific protease inhibitors. In this mini-review, we provide a phylogenomic overview of malarial proteases. An evolutionary perspective on the origin and divergence of these proteases will provide insights into the adaptive mechanisms of parasite growth, development, infection, and pathogenesis.

In silico Guided Drug Repurposing: Discovery of New Competitive and Non-competitive Inhibitors of Falcipain-2

Malaria is among the leading causes of death worldwide. The emergence of Plasmodium falciparum resistant strains with reduced sensitivity to the first line combination therapy and suboptimal responses to insecticides used for Anopheles vector management have led to renewed interest in novel therapeutic options. Here, we report the development and validation of an ensemble of ligand-based computational models capable of identifying falcipain-2 inhibitors, and their subsequent application in the virtual screening of DrugBank and Sweetlead libraries. Among four hits submitted to enzymatic assays, two (odanacatib, an abandoned investigational treatment for osteoporosis and bone metastasis, and the antibiotic methacycline) confirmed inhibitory effects on falcipain-2, with Ki of 98.2 nM and 84.4 μM. Interestingly, Methacycline proved to be a non-competitive inhibitor (α = 1.42) of falcipain-2. The effects of both hits on falcipain-2 hemoglobinase activity and on the development of P. falciparum were also studied.Fil: Alberca, Lucas Nicolás. Universidad Nacional de La Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Chuguransky, Sara Rocío. Universidad Nacional de La Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Alvarez, Cora Lilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Talevi, Alan. Universidad Nacional de La Plata; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Salas Sarduy, Emir. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentin

Optimization of Clustering and Database Screening Procedures for Cavbase and Virtual Screening for Novel Antimalarial and Antibacterial Molecules

Im Zyklus der rationellen Arzneimittelentwicklung werden Affinität und Selektivität von potentiellen Wirkstoffen intensiv erforscht. Da diese beiden Eigenschaften keine lineare Abhängigkeit zueinander aufweisen, führt höhere Affinität nicht gezwungenermaßen auch zu einer höheren Selektivität. Computer-basierte Verfahren spielen eine immer größere Rolle für die Analyse und Vorhersage von Selektivitätsprofilen. Da die meisten erfolgreich eingesetzten niedermolekularen Arzneistoffe in Vertiefungen auf Proteinoberflächen binden, spielen physiko-chemische Eigenschaften von Bindetaschen eine zentrale Rolle in der Erkennung und damit auch der Bindung von Liganden. Cavbase ist eine Methode, die es ermöglicht Bindetaschen anhand der physiko-chemischen Eigenschaften dort exponierter Aminosäuren zu beschreiben und unabhängig von ihrer Proteinsequenz und Faltungsgeometrie zu vergleichen. Die Bindetaschen-basierte Klassifizierung von Proteinen ist ein effektiver Ansatz, um relevante Informationen für Selektivitätsanalysen zu extrahieren, die durch Anwendung von Clustermethoden erreicht werden kann. In der vorliegenden Arbeit wurde ein neuartiger Arbeitsablauf zur Untersuchung von wichtigen Parametern einer Clusterung entwickelt. Für einen Datensatz von Proteinen wird eine Ähnlichkeitsmatrix berechnet und anschließend dem entwickelten Arbeitsablauf übergeben. Dieser Ansatz wurde erfolgreich an zwei unterschiedlichen Datensätzen getestet. Die vorhergesagte Anzahl der Cluster, die am besten geeignete Clustermethode und die anschließende Clusterstruktur waren in Übereinstimmung mit den Referenzklassifikation der Proteine. Im Falle der Protease-Proteinfamilie führte die Bindetaschen-basierte Klassifizierung zur einer signifikanten Gruppierung von Proteineinträgen, die unabhängig von Sequenzinformation entstanden. Damit konnte auf struktureller Ebene die Kreuzreaktivität zwischen dem Protein Calpain-1 und Cysteincathepsinen detektiert werden, die bis jetzt nur auf Basis von Liganddaten beschrieben wurde. Im weiteren Verlauf wurden elf unterschiedliche Serinproteasen untersucht, indem die Topologie der Liganden, Bindetaschen- und Sequenzinformationen miteinander verglichen wurden. Die entstandenen Cluster zeigen einen Korrelationstrend zwischen der Ähnlichkeit im Liganden- und Bindetaschenraum. Eine steigende Anzahl von Resistenzen auf derzeitig angewandte antiparasitäre und antibakterielle Arzneistoffe erfordert die Entwicklung neuartiger Antiinfektiva. Für den Parasiten Plasmodium falciparum, den Erreger der Malaria, wurde das Schlüsselenzym der Fettsäuresynthese Typ-2, Enoyl ACP Reduktase (ENR), als potentielle Zielstruktur vorgeschlagen. In einem virtuellen Screening einer virtuellen Datenbank von fragmentartigen Kleinmolekülen konnten acht vielversprechende Strukturen ausfindig gemacht werden. Ein Salicylsäureamidderivat zeigte in einem zellulären Assay inhibitorische Wirkung im erythrozytären Stadium. Diese Verbindung wurde in weiteren Schritten optimiert, in dem Struktur-Aktivitäts-Beziehungen und kombinatorisches Docking für Salicylamide analysiert wurden. Aus dieser Studie konnten zwei potente Verbindungen hervorgehen, die eine niedrige Zytotoxizität aufweisen und in einstellig mikromolarer Konzentration sowohl im erythrozytären als auch im prä-erythrozytären Stadium ihre hemmende Wirkung entfalten. Die Wirkung im prä-erythrozytären Stadium zeigte sich der Wirkung von Primaquin überlegen. Die Biosynthese der Tetrahydrofolsäure ist ein essenzieller Stoffwechselweg für fast alle Organismen. Das Enzym Pyruvoyltetrahydropterin Synthase im Plasmodium falciparum (PfPTPS) übernimmt in diesem Stoffwechselweg die Katalyse einer Reaktion, die gewöhnlich von Dihydroneopterin Aldolase katalysiert wird, das jedoch im Plasmodium Genom fehlt. Die Einbettung des Enzyms PfPTPS in den Folatstoffwechsel qualifiziert es als eine potentielle Zielstruktur zur Entwicklung neuartiger Antifolate. Eine spezielle auf dieses Zielprotein hin aufgearbeitete Bibliothek weist Kleinmoleküle mit zink-bindenden funktionellen Gruppen auf. Die Durchführung eines virtuellen Screenings führte zur Auswahl von neun Molekülen für die Synthese, die anschließend auf ihre biologische Wirkung evaluiert werden sollen. Eine Vielzahl pathogener Mikroorganismen sind auf die Synthese der Isoprenoide aus dem Methylerithritolphosphatweg (MEP-Weg) angewiesen, daher eignet sich die Inhibition dieses Stoffwechselweges als eine sinnvolle Strategie für die Wirkstoffentwicklung. IspD ist eines der Enzyme des MEP-Weges und wurde als Modellprotein zur Untersuchung der bestimmenden Faktoren für eine strukturbasierte Wirkstoffentwickung ausgewählt. Ein Datensatz von leitstrukturartigen Kleinmolekülen aus der ZINC Datenbank wurde für ein virtuelles Screening benutzt, das zur Auswahl von sieben Kandidaten führte. Sechs Verbindungen konnten kommerziell erworben und getestet werden. Für drei Verbindungen konnte eine Proteinbindung gemessen werden

Structural Insights Into Key Plasmodium Proteases as Therapeutic Drug Targets

Malaria, caused by protozoan of genus Plasmodium, remains one of the highest mortality infectious diseases. Malaria parasites have a complex life cycle, easily adapt to their host’s immune system and have evolved with an arsenal of unique proteases which play crucial roles in proliferation and survival within the host cells. Owing to the existing knowledge of enzymatic mechanisms, 3D structures and active sites of proteases, they have been proven to be opportune for target based drug development. Here, we discuss in depth the crucial roles of essential proteases in Plasmodium life cycle and particularly focus on highlighting the atypical “structural signatures” of key parasite proteases which have been exploited for drug development. These features, on one hand aid parasites pathogenicity while on the other hand could be effective in designing targeted and very specific inhibitors for counteracting them. We conclude that Plasmodium proteases are suitable as multistage targets for designing novel drugs with new modes of action to combat malaria

Structure-based drug discovery for tropical diseases

Parasitic diseases are amongst the foremost threats to human health and welfare around the world. In tropical and subtropical regions of the world, the consequences of parasitic infections are devastating both in terms of human morbidity and mortality. The current available drugs are limited, ineffective, and require long treatment regimens. To overcome these limitations, the identification of new macromolecular targets and small-molecule modulators is of utmost importance. The advances in genomics and proteomics have prompted drug discovery to move toward more rational strategies. The increasing understanding of the fundamental principles of protein-ligand interactions combined with the availability of compound libraries has facilitated the identification of promising hits and the generation of high quality lead compounds for tropical diseases. This review presents the current progresses and applications of structure-based drug design (SBDD) for the discovery of innovative chemotherapy agents for a variety of parasitic diseases, highlighting the challenges, limitations, and future perspectives in medicinal chemistry.FAPESPCNP

Structure based docking and molecular dynamic studies of plasmodial cysteine proteases against a South African natural compound and its analogs:

Identification of potential drug targets as well as development of novel antimalarial chemotherapies with unique mode of actions due to drug resistance by Plasmodium parasites are inevitable. Falcipains (falcipain-2 and falcipain-3) of Plasmodium falciparum, which catalyse the haemoglobin degradation process, are validated drug targets. Previous attempts to develop peptide based drugs against these enzymes have been futile due to the poor pharmacological profiles and susceptibility to degradation by host enzymes. This study aimed to identify potential non-peptide inhibitors against falcipains and their homologs from other Plasmodium species

Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement

Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models

La click-chemistry en el descubrimiento de fármacos

La revisión bibliográfica que se presenta a continuación trata sobre la llamada clickchemistry y su aplicación en el descubrimiento de fármacos. Para ello se parte de la definición de click-chemistry y sus principales características que la hacen adecuada para el descubrimiento de fármacos. En segundo lugar, se nombran algunas de sus múltiples aplicaciones además del descubrimiento de fármacos, concretamente de su utilidad en el etiquetado de biomoléculas, la síntesis y modificación de polímeros o la síntesis de ADN y ARN biocompatible. Posteriormente pasaremos a la aplicación de la click chemistry en el descubrimiento de fármacos, sobre la cual se basa esta revisión bibliográfica. Primero pasaremos a describir las tres estrategias principales a seguir en la síntesis de nuevos fármacos con click chemistry que son el cribado de alto rendimiento, la estrategia basada en fragmentos y la estrategia basada en fragmentos dinámica en molde. A continuación pasaremos a detallar múltiples ejemplos de inhibidores enzimáticos sintetizados con estas reacciones click como inhibidores de reductasas o de proteina quinasas entre otros. También se nombran algunos agonistas y antagonistas de receptores sintetizados con estas reacciones Por último se presentan las conclusiones sacadas de la revisión bibliográfica respecto a la click chemistry en el descubrimiento de fármacosUniversidad de Sevilla. Grado en Farmaci

Protease-associated cellular networks in malaria parasite Plasmodium falciparum

Abstract Background Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species 123, providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database 4, and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system 5, blood stage microarray experiments 678, proteomics 9101112, literature text mining, and sequence homology analysis. Seventy-seven (77) out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs). These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins), range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide processing, cell cycle progression, transcriptional regulation, and signal transduction networks. Conclusions Our network analysis of proteases from P. falciparum uses a so-called guilt-by-association approach to extract sets of proteins from the proteome that are candidates for further study. Novel protease targets and previously unrecognized members of the protease-associated sub-systems provide new insights into the mechanisms underlying parasitism, pathogenesis and virulence.</p