Fragment‐based drug discovery has gained a foothold in today's lead identification processes. We present the application of in silico fragment‐based screening for the discovery of novel lead compounds for the metalloendoproteinase thermolysin. We have chosen thermolysin to validate our screening approach as it is a well‐studied enzyme and serves as a model system for other proteases. A protein‐targeted virtual library was designed and screening was carried out using the program AutoDock. Two fragment hits could be identified. For one of them, the crystal structure in complex with thermolysin is presented. This compound was selected for structure‐based optimization of binding affinity and improvement of ligand efficiency, while concomitantly keeping the fragment‐like properties of the initial hit. Redesigning the zinc coordination group revealed a novel class of fragments possessing Ki values as low as 128 μM, thus they provide a good starting point for further hit evolution in a tailored lead design.

The development of farnesyltransferase inhibitors directed against Plasmodium falciparum is a strategy towards new drugs against malaria. Previously, we described benzophenone-based farnesyltransferase inhibitors with high in vitro antimalarial activity but no in vivo activity. Through the introduction of a methylpiperazinyl moiety, farnesyltransferase inhibitors with in vivo antimalarial activity were obtained. Subsequently, a structure-based design approach was chosen to further improve the antimalarial activity of this type of inhibitor. As no crystal structure of the farnesyltransferase of the target organism is available, homology modeling was used to reveal differences between the active sites of the rat/human and the P. falciparum farnesyltransferase. Based on flexible docking data, the piperazinyl moiety was replaced by a N,N,N'-trimethylethylenediamine moiety. This resulted in an inhibitor with significantly improved in vitro and in vivo antimalarial activity. Furthermore, this inhibitor displayed a notable increase in selectivity towards malaria parasites relative to human cells.

Fosmidomycin and its homologue FR900098 are inhibitors of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, which is part of the mevalonate-independent isoprenoid biosynthetic pathway. Replacement of the phosphonate moiety by uncharged sulfone or sulfonamide partial structures resulted in complete loss of activity. Dropping one of the two negative charges resulted in a marked decrease in activity. Through occupation of a hydrophobic binding site, some activity could be regained, leading to compounds with micromolar activity against cultured malaria parasites.

1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) represents an essential enzyme of the mevalonate-independent pathway of the isoprenoid biosynthesis. Using fosmidomycin as a specific inhibitor of Dxr, this enzyme was previously validated as target for the treatment of malaria and bacterial infections. The replacement of the formyl residue of fosmidomycin by spacious acyl residues yielded inhibitors active in the micromolar range. As predicted by flexible docking, evidence was obtained for the formation of a hydrogen bond between an appropriately placed carbonyl group in the acyl residue and the main-chain NH of Met214 located in the flexible catalytic loop of the enzyme.

Taking into account dynamical behavior and/or structural inaccuracies of receptor-ligand systems becomes increasingly important in structure-based drug design. Here, we describe the development of consensus Adaptation of Fields for Molecular Comparison (AFMoC) (abbreviated as AFMoCcon) models that account for multiple ligand conformations in an ensemble of protein configurations. Ligand and receptor conformational variability is considered in a "reverse", protein-based CoMFA-type approach that results in a tailor-made scoring function. As an extension to the current AFMoC approach, AFMoCcon applies partial-least-squares regression considering multimode binding and a variable influence on the model-based region selection to an extended descriptor matrix. The approach was validated on a dataset of 79 structurally diverse thrombin inhibitors, aligned either in an experimentally determined thrombin structure or superimpositions of three structurally diverse thrombin structures derived by homology modeling. Initially, robust AFMoC models could be obtained for the experimental (q2 = 0.57) and one of the modeled protein structures (q2 = 0.61). However, no relationship between the quality of the homology model and the AFMoC model could be observed, rendering the a priori choice of a single receptor structure a difficult task. Convincingly, a consensus AFMoC model based on the newly developed approach circumvents this problem and shows a comparable internal and external predictivity (q2 = 0.61) like the best model derived from conventional AFMoC. As further advantages, (i) the influence of the single receptor structure-ligand alignment (RSLA) on the AFMoCcon model can be determined, (ii) there is no principal limitation regarding the number of different RSLA considered, and (iii) AFMoCcon models can be interpreted in terms of contour plots that aid in proposing variations of the ligand structure to improve binding. We expect the AFMoCcon approach also to be valuable in those cases where multiple experimental receptor conformations are given.

We present structure-activity relationships for 43 inhibitors of 1-deoxyxylulose-5-phosphate (DOXP)-reductoisomerase, derived from protein-based docking, ligand-based 3D QSAR, and a combination of both approaches as realized by AFMoC (adaptation of fields for molecular comparison). DOXP-reductoisomerase (DXR) is a key enzyme of the non-mevalonate pathway for isoprenoid building blocks. This target has been characterized as having potential in the treatment of malaria with fosmidomycin, an established DXR inhibitor, presently in clinical trials. As part of an effort to optimize the properties of fosmidomycin, analogues have been synthesized and tested to gain further insights into the primary determinants of structural affinity. These data have been used to create a predictive model for DXR inhibition applying data taken from several DXR X-ray structures. These structures still leave the active fosmidomycin conformation and detailed reaction mechanism undetermined. This together with the small inhibitor data set provides a major challenge for presently available docking programs and 3D QSAR tools. To overcome these difficulties we have applied the AFMoC protocol. AFMoC makes more efficient use of available modeling data by tailoring DrugScore knowledge-based potentials specifically toward a given protein using inhibitor potency data. While 3D QSAR methods achieved valid models which lack predictivity, AFMoC was found to provide superior performance, based both on cross-validation runs as well as for inhibitors not considered in the training set. In particular, AFMoC's ability to gradually transform between generally applicable unadapted interaction fields to case specifically adapted ones proved to be of major importance. Using 50% tailored fields was found to permit the precise prediction of binding affinities for related ligands without losing the capability to estimate the affinities of structurally distinct inhibitors.

Chalcone synthases (CHSs) and acridone synthases (ACSs) belong to the superfamily of type III polyketide synthases (PKSs) and condense the starter substrate 4-coumaroyl-CoA or N-methylanthraniloyl-CoA with three malonyl-CoAs to produce flavonoids and acridone alkaloids, respectively. ACSs which have been cloned exclusively from Ruta graveolens share about 75-85% polypeptide sequence homology with CHSs from other plant families, while 90% similarity was observed with CHSs from Rutaceae, i.e., R. graveolens, Citrus sinensis and Dictamnus albus. CHSs cloned from many plants do not accept N-methylanthraniloyl-CoA as a starter substrate, whereas ACSs were shown to possess some side activity with 4-coumaroyl-CoA. The transformation of an ACS to a functional CHS with 10% residual ACS activity was accomplished previously by substitution of three amino acids through the corresponding residues from Ruta-CHS1 (Ser132Thr, Ala133Ser and Val265Phe). Therefore, the reverse triple mutation of Ruta-CHS1 (mutant R2) was generated, which affected only insignificantly the CHS activity and did not confer ACS activity. However, competitive inhibition of CHS activity by N-methylanthraniloyl-CoA was observed for the mutant in contrast to wild-type CHSs. Homology modeling of ACS2 with docking of 1,3-dihydroxy-N-methylacridone suggested that the starter substrates for CHS or ACS reaction are placed in different topographies in the active site pocket. Additional site specific substitutions (Asp205Pro/Thr206Asp/His207Ala or Arg60Thr and Val100Ala/Gly218Ala, respectively) diminished the CHS activity to 75-50% of the wild-type CHS1 without promoting ACS activity. The results suggest that conformational changes in the periphery beyond the active site cavity volumes determine the product formation by ACSs vs. CHSs in R. graveolens. It is likely that ACS has evolved from CHS, but the sole enlargement of the active site pocket as in CHS1 mutant R2 is insufficient to explain this process.

We have designed the nitrophenylfurylacryl-substituted benzophenone 4f as a non-thiol farnesyltransferase inhibitor utilizing a novel aryl binding site of farnesyltransferase. Variation of the 2-acylamino substituent at the benzophenone core structure of our initial lead 4f yielded several non-thiol farnesyltransferase inhibitors with improved activity. These compounds display activity in the low nanomolar range.

The inhibition of farnesyltransferase was recently suggested as a new strategy for malaria therapy. A class of farnesyltransferase inhibitors such as 1 has been prepared which have in vivo activity in a murine malaria model. These inhibitors significantly reduce the farnesylation of parasite proteins.

We have designed arylfurylacryl-substituted benzophenones as non-thiol farnesyltransferase inhibitors utilizing a novel aryl binding site of farnesyltransferase. These compounds display activity in the low nanomolar range.

We recently described two novel aryl binding sites of farnesyltransferase. In this study, the cinnamoyl residue was designed as an appropriate substituent for our benzophenone-based AAX-peptidomimetic compound capable of occupying the far aryl binding site.

Angewandte ChemieVolume 116, Issue 2 p. 254-257 Zuschrift Farnesyltransferase-Inhibitoren hemmen das Wachstum von Malaria-Erregern in vitro und in vivo† Jochen Wiesner Dr., Jochen Wiesner Dr. Biochemisches Institut der Justus-Liebig-Universität Gießen, Friedrichstraße 24, 35392 Gießen, DeutschlandSearch for more papers by this authorKatja Kettler, Katja Kettler Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorJacek Sakowski Dr., Jacek Sakowski Dr. Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorRegina Ortmann Dr., Regina Ortmann Dr. Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorAlejandro M. Katzin Prof. Dr., Alejandro M. Katzin Prof. Dr. Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Professor Lineu Prestes, 1374, CEP 05508-900, São Paulo, BrasilienSearch for more papers by this authorEmília A. Kimura Dr., Emília A. Kimura Dr. Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Professor Lineu Prestes, 1374, CEP 05508-900, São Paulo, BrasilienSearch for more papers by this authorKatrin Silber, Katrin Silber Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, DeutschlandSearch for more papers by this authorGerhard Klebe Prof Dr., Gerhard Klebe Prof Dr. Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, DeutschlandSearch for more papers by this authorHassan Jomaa Dr., Hassan Jomaa Dr. Biochemisches Institut der Justus-Liebig-Universität Gießen, Friedrichstraße 24, 35392 Gießen, DeutschlandSearch for more papers by this authorMartin Schlitzer Prof. Dr., Martin Schlitzer Prof. Dr. [email protected] Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this author Jochen Wiesner Dr., Jochen Wiesner Dr. Biochemisches Institut der Justus-Liebig-Universität Gießen, Friedrichstraße 24, 35392 Gießen, DeutschlandSearch for more papers by this authorKatja Kettler, Katja Kettler Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorJacek Sakowski Dr., Jacek Sakowski Dr. Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorRegina Ortmann Dr., Regina Ortmann Dr. Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this authorAlejandro M. Katzin Prof. Dr., Alejandro M. Katzin Prof. Dr. Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Professor Lineu Prestes, 1374, CEP 05508-900, São Paulo, BrasilienSearch for more papers by this authorEmília A. Kimura Dr., Emília A. Kimura Dr. Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Av. Professor Lineu Prestes, 1374, CEP 05508-900, São Paulo, BrasilienSearch for more papers by this authorKatrin Silber, Katrin Silber Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, DeutschlandSearch for more papers by this authorGerhard Klebe Prof Dr., Gerhard Klebe Prof Dr. Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, DeutschlandSearch for more papers by this authorHassan Jomaa Dr., Hassan Jomaa Dr. Biochemisches Institut der Justus-Liebig-Universität Gießen, Friedrichstraße 24, 35392 Gießen, DeutschlandSearch for more papers by this authorMartin Schlitzer Prof. Dr., Martin Schlitzer Prof. Dr. [email protected] Ludwig-Maximilians-Universität München, Department Pharmazie – Zentrum für Pharmaforschung, Butenandtstraße 5–13, 81377 München, Deutschland, Fax: (+49) 89-2180-79992Search for more papers by this author First published: 19 December 2003 https://doi.org/10.1002/ange.200351169Citations: 11 † Diese Arbeit wurde durch das INCO-Dev-Programm im fünften Rahmenprogramm der Europäischen Kommission gefördert (Vertrags-Nr. ICA4-CT-2001-10078). Wir danken Dajana Henschker für hervorragende technische Assistenz. Read the full textAboutPDF ToolsRequest permissionAdd to favorites ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat Graphical Abstract Die Hemmung der Farnesyltransferase wurde kürzlich als neues Prinzip in der Malariatherapie vorgeschlagen. Die hier vorgestellten Farnesyltransferase-Inhibitoren, z. B. 1, sind in vitro und erstmalig auch im Mausmodell gegen Plasmodien wirksam und reduzieren die Farnesylierung von Parasiten-Proteinen signifikant. References 1H.-W. Fu, P. J. Casey, Recent Prog. Horm. 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