Synthesis, Characterization, and in vivo Evaluation of a Novel Potent Autotaxin-Inhibitor

The autotaxin-lysophosphatidic acid (ATX-LPA) signaling pathway plays a role in a variety of autoimmune diseases, such as rheumatoid arthritis or neurodegeneration. A link to the pathogenesis of glaucoma is suggested by an overactive ATX-LPA axis in aqueous humor samples of glaucoma patients. Analysis of such samples suggests that the ATX-LPA axis contributes to the fibrogenic activity and resistance to aqueous humor outflow through the trabecular meshwork. In order to inhibit or modulate this pathway, we developed a new series of ATX-inhibitors containing novel bicyclic and spirocyclic structural motifs. A potent lead compound (IC50 against ATX: 6 nM) with good in vivo PK, favorable in vitro property, and safety profile was generated. This compound leads to lowered LPA levels in vivo after oral administration. Hence, it was suitable for chronic oral treatment in two rodent models of glaucoma, the experimental autoimmune glaucoma (EAG) and the ischemia/reperfusion models. In the EAG model, rats were immunized with an optic nerve antigen homogenate, while controls received sodium chloride. Retinal ischemia/reperfusion (I/R) was induced by elevating the intraocular pressure (IOP) in one eye to 140 mmHg for 60 min, followed by reperfusion, while the other untreated eye served as control. Retinae and optic nerves were evaluated 28 days after EAG or 7 and 14 days after I/R induction. Oral treatment with the optimized ATX-inhibitor lead to reduced retinal ganglion cell (RGC) loss in both glaucoma models. In the optic nerve, the protective effect of ATX inhibition was less effective compared to the retina and only a trend to a weakened neurofilament distortion was detectable. Taken together, these results provide evidence that the dysregulation of the ATX-LPA axis in the aqueous humor of glaucoma patients, in addition to the postulated outflow impairment, might also contribute to RGC loss. The observation that ATX-inhibitor treatment in both glaucoma models did not result in significant IOP increases or decreases after oral treatment indicates that protection from RGC loss due to inhibition of the ATX-LPA axis is independent of an IOP lowering effect.

The Playbooks of Medicinal Chemistry Design Moves

Large databases of biologically relevant molecules, such as ChEMBL, SureChEMBL, or compound collections of pharmaceutical or agrochemical companies, are invaluable sources of medicinal chemistry information, albeit implicit. We developed a modified matched molecular pair approach to systematically and exhaustively extract the transformations in these databases and distill them into snippets of explicit design knowledge that are easily interpretable and directly applicable. The resulting "playbooks of medicinal chemistry design moves" capture the collective pharmaceutical and agrochemical research expertise across multiple chemists, companies, targets, and projects. They can be queried in an automated fashion for systematic prospective design and compound generation. The ChEMBL playbook and an application to exploit it are available at https://github.com/mahendra-awale/medchem_moves.

Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors

Improving the binding affinity of a chemical series by systematically probing one of its exit vectors is a medicinal chemistry activity that can benefit from molecular modeling input. Herein, we compare the effectiveness of four approaches in prioritizing building blocks with better potency: selection by a medicinal chemist, manual modeling, docking followed by manual filtering, and free energy calculations (FEP). Our study focused on identifying novel substituents for the apolar S2 pocket of cathepsin L and was conducted entirely in a prospective manner with synthesis and activity determination of 36 novel compounds. We found that FEP selected compounds with improved affinity for 8 out of 10 picks compared to 1 out of 10 for the other approaches. From this result and other additional analyses, we conclude that FEP can be a useful approach to guide this type of medicinal chemistry optimization once it has been validated for the system under consideration.

A Real-World Perspective on Molecular Design

We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

Predicting new molecular targets for known drugs

Whereas drugs are intended to be selective, at least some bind to several physiologic targets, explaining both side effects and efficacy. As many drug-target combinations exist, it would be useful to explore possible interactions computationally. Here, we compared 3,665 FDA-approved and investigational drugs against hundreds of targets, defining each target by its ligands. Chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations. Thirty were tested experimentally, including the antagonism of the β₁ receptor by the transporter inhibitor Prozac, the inhibition of the 5-HT transporter by the ion channel drug Vadilex, and antagonism of the histamine H₄ receptor by the enzyme inhibitor Rescriptor. Overall, 23 new drug-target associations were confirmed, five of which were potent (< 100 nM). The physiological relevance of one such, the drug DMT on serotonergic receptors, was confirmed in a knock-out mouse. The chemical similarity approach is systematic and comprehensive, and may suggest side-effects and new indications for many drugs.

Quantifying biogenic bias in screening libraries

In lead discovery, libraries of 10⁶ molecules are screened for biological activity. Given the over 10⁶⁰ drug-like molecules thought possible, such screens might never succeed. That they do, even occasionally, implies a biased selection of library molecules. Here a method is developed to quantify the bias in screening libraries towards biogenic molecules. With this approach, we consider what is missing from screening libraries and how they can be optimized.

Off-target networks derived from ligand set similarity

Chemically similar drugs often bind biologically diverse protein targets, and proteins with similar sequences or structures do not always recognize the same ligands. How can we uncover the pharmacological relationships among proteins, when drugs may bind them in defiance of bioinformatic criteria? Here we consider a technique that quantitatively relates proteins based on the chemical similarity of their ligands. Starting with tens of thousands of ligands organized into sets for hundreds of drug targets, we calculated the similarity among sets using ligand topology. We developed a statistical model to rank the resulting scores, which were then expressed in minimum spanning trees. We have shown that biologically sensible groups of targets emerged from these maps, as well as experimentally validated predictions of drug off-target effects.

Quantifying the relationships among drug classes

The similarity of drug targets is typically measured using sequence or structural information. Here, we consider chemo-centric approaches that measure target similarity on the basis of their ligands, asking how chemoinformatics similarities differ from those derived bioinformatically, how stable the ligand networks are to changes in chemoinformatics metrics, and which network is the most reliable for prediction of pharmacology. We calculated the similarities between hundreds of drug targets and their ligands and mapped the relationship between them in a formal network. Bioinformatics networks were based on the BLAST similarity between sequences, while chemoinformatics networks were based on the ligand-set similarities calculated with either the Similarity Ensemble Approach (SEA) or a method derived from Bayesian statistics. By multiple criteria, bioinformatics and chemoinformatics networks differed substantially, and only occasionally did a high sequence similarity correspond to a high ligand-set similarity. In contrast, the chemoinformatics networks were stable to the method used to calculate the ligand-set similarities and to the chemical representation of the ligands. Also, the chemoinformatics networks were more natural and more organized, by network theory, than their bioinformatics counterparts: ligand-based networks were found to be small-world and broad-scale.

New methods for ligand-based virtual screening: use of data fusion and machine learning to enhance the effectiveness of similarity searching

Similarity searching using a single bioactive reference structure is a well-established technique for accessing chemical structure databases. This paper describes two extensions of the basic approach. First, we discuss the use of group fusion to combine the results of similarity searches when multiple reference structures are available. We demonstrate that this technique is notably more effective than conventional similarity searching in scaffold-hopping searches for structurally diverse sets of active molecules; conversely, the technique will do little to improve the search performance if the actives are structurally homogeneous. Second, we make the assumption that the nearest neighbors resulting from a similarity search, using a single bioactive reference structure, are also active and use this assumption to implement approximate forms of group fusion, substructural analysis, and binary kernel discrimination. This approach, called turbo similarity searching, is notably more effective than conventional similarity searching.

Enhancing the Effectiveness of Similarity-Based Virtual Screening Using Nearest-Neighbor Information

We test the hypothesis that fusing the outputs of similarity searches based on a single bioactive reference structure and on its nearest neighbors (of unknown activity) is more effective (in terms of numbers of high-ranked active structures) than a similarity search involving just the reference structure. This turbo similarity searching approach provides a simple way to enhance the effectiveness of simulated virtual screening searches of the MDL Drug Data Report database.

Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures

This paper reports a detailed comparison of a range of different types of 2D fingerprints when used for similarity-based virtual screening with multiple reference structures. Experiments with the MDL Drug Data Report database demonstrate the effectiveness of fingerprints that encode circular substructure descriptors generated using the Morgan algorithm. These fingerprints are notably more effective than fingerprints based on a fragment dictionary, on hashing and on topological pharmacophores. The combination of these fingerprints with data fusion based on similarity scores provides both an effective and an efficient approach to virtual screening in lead-discovery programmes.

Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures

Fingerprint-based similarity searching is widely used for virtual screening when only a single bioactive reference structure is available. This paper reviews three distinct ways of carrying out such searches when multiple bioactive reference structures are available: merging the individual fingerprints into a single combined fingerprint; applying data fusion to the similarity rankings resulting from individual similarity searches; and approximations to substructural analysis. Extended searches on the MDL Drug Data Report database suggest that fusing similarity scores is the most effective general approach, with the best individual results coming from the binary kernel discrimination technique.

[Meniscoids of the intervertebral joints]

PURPOSE OF THE STUDY

A large amount of material was used to study the distribution, location and shape of meniscoids in intervertebral joints of the human spine, from the atlanto-occipital joint to the sacrum, in order to find out how many of intervertebral joints had mobile meniscoids. These might be regarded as possible causes of spinal blockade or other vertebrogenous complaints.

MATERIAL

The materials provided by the Department of Anatomy and Department of Forensic Medicine at the Faculty of Medicine of Charles University in Pilznen included 20 cadaverous spines from humans aged 20 to 80 years.

METHODS

Access to each joint was provided by dissection of the articular capsule from the lower articular processes of the vertebra situated above. In the orthograde view, all meniscoids were described in terms of shape, size, consistence and location. Their structure was ascertained by histological examination of cross sections stained with haematoxylin and eosin.

RESULTS

Meniscoids varying in shape and size were found in all of the intervertebral joints. They were classified by their histological structure as synovial, fat and fibrous meniscoids. The first category was observed frequently, the last only rarely. A total of 29 mobile meniscoids were recorded, most of them in the lumbar spine. Most of the meniscoids present in the cervical spine were of synovial and less frequently of fat types. Meniscoids found in the thoracic spine were poorly developed synovial ones and those present in the lumbar spine were of all types and were also largest in size. The most conspicuous meniscoids were seen in the spines that showed degenerative changes in intervertebral joints. Large fat pads were found in atlanto-occipital and atlanto-axial joints. Mobile meniscoids, most of them present in the lumbar spine (6.4% of all joints.), were connected with the capsule by a thin pedicle and it was possible to move them over a half of the articular surface. Some inter-individual changes were also found; in some spines, the most developed meniscoids were fat pads, in the others, these were synovial meniscoids. Spines of younger individuals showed a predominance of synovial meniscoids with smooth surfaces that arched against the articular cavity. In spines of elderly individuals, meniscoids were rough, in some cases fibrous in structure, and had a lobulated or frayed edge.

DISCUSSION

The shape, location of meniscoids and their presence in every joint indicate their definite role for the spine: they compensate the incongruence of articular surfaces, fill in empty spaces and facilitate spread of synovial fluid during translation movements. Variability in shape, size and location of meniscoids give support to the view that meniscoids developed secondarily in relation to the morphogenesis of articular surfaces and that they are fully adapted to the shape and function of the joint. Mobile meniscoids, particularly fibrous ones, can get wedged between articular surfaces due to a sudden, rush movement (entrapment theory) or can be caught between the edge of an articular surface and the articular capsule attachment (extrapment theory). This situation may result in either mechanical or functional blockade of the spine and a subsequent painful condition due to compression of nerves and reflex contraction of muscles. Direct evidence of such blockade and the validity of either hypothesis can today be provided by magnetic resonance imaging.

CONCLUSIONS

All intervertebral joints, along the length of spine, possess capsule processes, i.e., meniscoids, which can be classified as synovial, fat and fibrous. Meniscoids are most developed in the lumbar and cervical spine. They serve to compensate for the incongruence of articular surfaces and to fill in empty spaces. Mobile, peduncular meniscoids can, at sudden or non-physiological movements, be caught between articular surfaces and cause spinal blockade and painful conditions. Manipulative treatment is, therefore, justified in indicated cases.

[Mechanical loading of the human femoral neck]

PURPOSE OF THE STUDY

The aim of the study is to explain what is the actual loading of human proximal femur.

MATERIAL

Measuring of stress is based on 5 femurs of normal shape (bones obtained from dissection and ossuary). In order to determine the direction of the resultant force the authors used 30 ossuary bones of different age but of analogical shape.

METHODS

By means of their own graphic method the authors identified the direction of appositional growth of femoral neck which contains with the longitudinal diaphyseal axis the angle of 26 degrees (alpha angle). The value of the angle is identical with the direction of the resultant force acting on the femoral head in vivo. Tensometric method was used for the measuring of stress on the medial and lateral surfaces of femoral neck during loading in direction of the determined resultant force. Linear strain gauges of Hottinger type were used for the measuring and Instron apparatus was applied for biomechanical analysis in which femoral heads were loaded by a standard force of 50 kg, first in the direction of femoral diaphyseal axis and then gradually (always by 5 degrees) in the divergence from the diaphyseal axis up to 50 degrees.

RESULTS

Appositional growth of femoral neck with regard to the longitudinal diaphyseal axis is progressing under the alpha angle (alpha = 26 degrees), which corresponds to the direction of the resultant force. The value of the compression stress on the medial surface of the neck ranged between--165 and -300 microstrain (mean value -239 microstrain). On the lateral surface there is a tension stress ranging between +20 up to +140 microstrain (main value +64 microstrain). The ratio of stress on both sides (surfaces) was 3.8:1. The point of zero stress is located in the lateral part of the neck, i.e. in the area of lateral trajectorial system of cancellous bone.

DISCUSSION

The method of measuring of the direction of the resultant force on the basis of the bone development (on the basis of superposition of successive growth stages) is despite certain inaccuracies a correct procedure. The alpha angle (alpha = 26 degrees) identified by the authors corresponds with Pauwels' calculation (24 degrees) and Bergman's findings (22 degrees up to 27 degrees). The identified values of stress show that the opinion on a purely axial loading of the neck is wrong and has to be corrected. Femur is not exposed in the frontal plane to the action of the resultant force only in one direction as supposed e.g. by Pauwels but the direction of the resultant force oscillates within a limited extent from different directions. It means that the lateral wall of femoral neck is exposed to alternating both tensile and compression loading.

CONCLUSION

The presented work allows to specify the opinions on the way of loading of human proximal femur. Our experiments have shown that apart from axial pressure the femoral neck is exposed also to bending forces. This way of loading also corresponds with the oval shape and thickened medial wall of the neck.

[Dependence of mechanical strength on the architecture of the compact bone of human shaft.]

A secondarilly remodelled bone (the haversian bone) forming a wall of human shaft represents a significantly anisotropic material, which has different strengths in different directions. One of the factors influencing mechanical properties (strength in particular) of the bone is the architectonics of the compact bone. Osteons of the haversian bone are arranged in the direction of the dominant first principal stress and create two antirotational spiral systems in the opposite walls of the shaft. The aim of the work was to found out how the bone tensile strength depends on the orientation of osteons and check whether the premise applies that the architectonics of the haversian bone depends on the directions of the first principal stress and in what relation of strength moments the direction of the first principal stress corresponds to the actual orientation of osteons. The results of the tensile strength tests in wet samples from 10 femurs and the strength of the whole shaft in 9 pairs of femurs (cadaver material) have confirmed the premise that osteons are arranged in the directions of the dominant first principal stress and depend on the relation between bending and torsion moments. The strength of the femoral shaft is maximal in the physiological way of loading, i.e. in medial bending and outer rotation. The decisive motion on which the strength of the bone depends is torsion. In non-physiological loading the femoral shaft (by an opposite bending moment or opposite torsion moment in medial bending) the strength of the bone is significantly lower. From the biomechanical viewpoint the architecture of the haversian bone has an optimal and efficient structure. Key words: compact bone, bone strength, types of loading.

["Tension" and "pressure" osteons - reality or myth?]

The underlying study tests the hypothesis on the existence of two types of osteons, the "tension" and the "pressure" ones. Osteons of the first type should be built under the influence of tension and should manifest greater strength in tension. The contrary applies to the "pressure" osteons. The ultimate strength of the bone tissue in tension and compression was studied on samples from the medial wall of the femoral diaphysis, subjected in vivo to compression, and on samples from the lateral wall, subjected to tension. All samples were manufactured with the long axis corresponding to the orientation of osteons, arranged in two helical antirotary systems situated in the contralateral walls of the diaphysis. The osteon orientation was ascertained after filling vascular canals with India-ink. The bone samples were tested using the Schenk Trebel RM 10-K machine. Tension tests found no difference in bone strength between samples from the lateral and from the medial walls. In compression tests, three cases manifested greater strength in samples from the medial wall, two cases in samples from the lateral wall. Such results speak against the hypothesis of the existence of two functional types of osteons. A complementary series of experiments showed that the tension strength is greatest in samples having a longitudinal orientation of osteons and that it decreases rapidly with growing inclination of osteons from the axis of loading. The dominant factor, responsible for the bone strength, is therefore the osteon orientation and not the mode of mechanical loading in vivo or the orientation of collagen fibres. Key words: haversian bone, osteons, strength of bone.

Spatial organization of the haversian bone in man

The osteons in all human long bones are grouped in two helical antirotary systems of opposite oblique directions, situated in the contralateral walls of the diaphysis. Several arguments support the hypothesis that this special architecture arises from functional adaptations and that it depends on the orientation of the first principal stress. A new macroscopic method based on the filling of vascular canals of the undecalcified, polished bone with India-ink enabled us to study the spatial architecture of the haversian bone in the entire diaphysis. The osteon directions in normal and atypical femurs was compared with the direction of the first principal stresses, determined analytically in a cylindrical tube model of the diaphysis subjected to a combination of bending, torsion and compression. Under combined loading with the bending moment in the frontal plane to the medial side and with the torque moment in the sense of external rotation, the direction of the first principal stresses corresponded with the direction of osteons in the diaphysis of the femur. In both cases, the first principal stresses, as well as the osteons, were oriented in the opposite oblique direction in the medial and lateral walls of the model and of the bones. Between the two oblique fields a sharp boundary with an atypical organization of the principal stresses and osteons existed. In atypical femurs the osteonal orientation was longitudinal (likely unloaded femurs) or rotated 90 degrees (markedly anteriorly convex femurs). These observations support the hypothesis of a causal relation between the loading mode and the dominant osteonal direction. The organization of the haversian bone seems a typical example of functional adaptation.

Osteon orientation of the diaphysis of the long bones in man

The orientation of osteons has been described in the long bones of man, using a special macroscopic method, which enabled the study of the osteonal architecture throughout the extent of the diaphysis. The osteons in all bones are arranged in two helical systems of opposite directions, which lie on the opposite sides of the diaphysis. The inclination of osteon direction from the bone axis in remarkably constant, varying between 5 degrees and 15 degrees. The boundary between the two fields is sharp. This special type of osteon orientation corresponds with the directions of the maximum principal stress and/or strain in the walls of the bones, which are exposed to both the bending and torque moments. The typical orientation of osteons reflects the history of loading of the bones in the course of physiological activity. The dominant stress state of every bone could be deduced from the osteon orientation and from the position of the pressure and tension fields on the surface of the bone.

A new attempt at the interpretation of the functional architecture of the cancellous bone

The author's theory explains the development mechanisms of the functional structure of cancellous bone. Functional, secondary cancellous bone develops from the primary growth-dependent cancellous lattice under the influence of multidirectional loading. The primary cancellous bone is remodelled according to the general strain-dependent mechanism of the functional adaptation of bone. Oblique loading of the metaphysis in extreme positions in the joint evokes the greatest strain in the bone trabeculae oriented in these oblique directions, as demonstrated by calculation on a simple three-beam model. All trabeculae are therefore remodelled in these directions resulting in a typical picture of two crossed pressure systems. Each of them corresponds to one of the extreme loading directions. Tensile systems can be found only in places of ligament or tendon insertions or under concave joint surfaces.

[Importance of vascular and mechanical factors for bone healing.]

The author submits a brief account of contemporary views on the importance of vascular and mechanical factors for healing of bones. Damage of the vascularization after fractures when using conservative treatment and intramedullary and external fixation, does not influence bone healing in a substantial way. In those instances the bone heals by forming a callus with newly formed ample vascularization. On the other hand, in case of osteosynthesis, using a splint with perfect stabilization, the bone heals very slowly by a process of direct healing by haver remodelling. The period of healing is proportional to the extent of bone necrosis. Therefore biological surgery with maximal sparing of periostal vessels is essential. The importance of mechanical factors depends also on the type of healing. The prerequisite of direct healing and healing in the cavity is mechanical rest. Mechanical influences become involved only in the osteoblastic, apposition stage of the remodelling process. During healing by means of a callus mechanical factors play a different role in different stages of development of the callus. In the proliferation stage the mechanical optimum is moderate, so far not accurately quantified motor activity. In the differentiation stage similar mechanisms are involved as during differentiation of the embryonic mesenchymal blastema: traction in the surface layers of the callus leads to desmogenesis, pressure inside the callus to chondrogenesis. The ossification stage calls for mechanical rest. In the final modelling and remodelling stage two basic mechanism of functional adaptation of bone are involved, apposition caused by deformation of the bone marrow and surface reabsorption caused by direct pressure of the adjacent periostium. In the conclusion the authors discuss the importance of mechanical factors in the stress shielding phenomenon, traction osteogenesis and dynamic compression. Key words: bone - healing, vascular and mechanical factors, mechanical factors - bone.

[Wolff's law of transformation after 100 years]

In the introduction to the article the author briefly describes the history of the Wolff's invention that under the influence of the function the bone structure is restructuring. This functional adaptation however, has not been fully clarified until these days. At present the general scheme of the fundamental adaptation mechanism has been generally adopted according to which the bone responds to the inner strain by aposition of the new bone while inactivity results in resorption. The author's own experiment as well as modern experiments carried out by the Lanyon group have proved that the starting point for reaction is intermittent loading in which both pressure and tension have the same effect. The strain results in the deformation of the bone tissue which is by an unclear yet way perceived and signalled to the superficial osteoblasts. However, not all cases of the functional adaptation of the bone can be explained in this way, first of all the remodelling of deformities after fractures or the modelling of metaphysis and the lateral drift of diaphysis in the course of normal growth. In comparison to Currey and other authors who therefore share the view that there does not exist a uniform algorithm of the functional adaptation of bone the author explains the functional adaptation by a uniform even if complex algorithm comprising apart from the reaction of the bone to the inner strain another two mechanisms: 1. Modelling of the bone surface by the periosteum. The increase in pressure between periosteum and bone results in resorption, avulsion of periosteum to the aposition of the new bone. 2. In the course of the growth another factor participates in the functional adaptation, namely the physeal plate, responding to loading according to Hüter-Volkmann's law: "Overload results in reducing of the growth, while relief in its acceleration". In oblique loading the plate changes, due to asymmetric loading, the direction of the growth precisely in the direction of the pressure resultant. Only by the cooperation of the three given mechanisms all cases of the functional adaptation of the bone can be explained.(ABSTRACT TRUNCATED AT 400 WORDS)