Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer.

SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein-ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3S,4S)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine (1), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.

Systematic Chemogenetic Library Assembly.

Chemogenetic libraries, collections of well-defined chemical probes, provide tremendous value to biomedical research but require substantial effort to ensure diversity as well as quality of the contents. We have assembled a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our approach, lessons learned, and disclosing our current collection of 4,185 compounds with their primary annotated gene targets (https://github.com/Novartis/MoaBox). This physical collection is regularly updated and used broadly both within Novartis and in collaboration with external partners.

A Novel Evidence Conflict Measurement for Multi-Sensor Data Fusion Based on the Evidence Distance and Evidence Angle.

As an important method for uncertainty modeling, Dempster-Shafer (DS) evidence theory has been widely used in practical applications. However, the results turned out to be almost counter-intuitive when fusing the different sources of highly conflicting evidence with Dempster's combination rule. In previous researches, most of them were mainly dependent on the conflict measurement method between the evidence represented by the evidence distance. However, it is inaccurate to characterize the evidence conflict only through the evidence distance. To address this issue, we comprehensively consider the impacts of the evidence distance and evidence angle on conflicts in this paper, and propose a new method based on the mutual support degree between the evidence to characterize the evidence conflict. First, the Hellinger distance measurement method is proposed to measure the distance between the evidence, and the sine value of the Pignistic vector angle is used to characterize the angle between the evidence. The evidence distance indicates the dissimilarity between the evidence, and the evidence angle represents the inconsistency between the evidence. Next, two methods are combined to get a new method for measuring the mutual support degree between the evidence. Afterward, the weight of each evidence is determined by using the mutual support degree between the evidence. Then, the weights of each evidence are utilized to modify the original evidence to achieve the weighted average evidence. Finally, Dempster's combination rule is used for fusion. Some numerical examples are given to illustrate the effectiveness and reasonability for the proposed method.

Maize productivity and soil properties in the Loess Plateau in response to ridge-furrow cultivation with polyethylene and straw mulch.

Ridge-furrow with full film mulching (RFFM) is widely used in the Loess Plateau (LP) to increase maize yield. However, continuous RFFM application may cause excessive depletion of soil organic carbon (SOC) and soil water storage (SWS). The present study tested four production systems, namely, (1) RFFM; (2) ridge-furrow with polyethylene film and straw mulching (RFFSM); (3) non-contoured seedbed with film mulching (FFM); and (4) non-contoured seedbed without mulching (CK) in 2013 and 2014 to identify an optimal technique to increase maize yield yet minimizing the negative effects. SWS under RFFSM was significantly higher by 5.4% and 13.4% compared to RFFM and CK, respectively. The changes in SOC were -0.2, -0.2, and -0.4 g·kg-1 for RFFM, FFM, and CK, respectively, and 0.3 g·kg-1 for RFFSM. Increased root residue and extra external carbon input to soil under RFFSM directly contributed to SOC recovery. RFFSM had a comparable grain yield but higher water use efficiency compared to RFFM. The combination of RFFSM is promising for improving SOC stocks, water storage, and maize productivity.

Discovery and Characterization of Allosteric WNK Kinase Inhibitors.

Protein kinases are known for their highly conserved adenosine triphosphate (ATP)-binding site, rendering the discovery of selective inhibitors a major challenge. In theory, allosteric inhibitors can achieve high selectivity by targeting less conserved regions of the kinases, often with an added benefit of retaining efficacy under high physiological ATP concentration. Although often overlooked in favor of ATP-site directed approaches, performing a screen at high ATP concentration or stringent hit triaging with high ATP concentration offers conceptually simple methods of identifying inhibitors that bind outside the ATP pocket. Here, we applied the latter approach to the With-No-Lysine (K) (WNK) kinases to discover lead molecules for a next-generation antihypertensive that requires a stringent safety profile. This strategy yielded several ATP noncompetitive WNK1-4 kinase inhibitors, the optimization of which enabled cocrystallization with WNK1, revealing an allosteric binding mode consistent with the observed exquisite specificity for WNK1-4 kinases. The optimized compound inhibited rubidium uptake by sodium chloride cotransporter 1 (NKCC1) in HT29 cells, consistent with the reported physiology of WNK kinases in renal electrolyte handling.

Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases.

The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS­ERK signalling pathway. It is also a key mediator of the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA) immune checkpoint pathways. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy. Here we report the discovery of a highly potent (IC50 = 0.071 µM), selective and orally bioavailable small-molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto-inhibited conformation. SHP099 concurrently binds to the interface of the N-terminal SH2, C-terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS­ERK signalling to inhibit the proliferation of receptor-tyrosine-kinase-driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.

Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor.

SHP2 is a nonreceptor protein tyrosine phosphatase (PTP) encoded by the PTPN11 gene involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also purportedly plays an important role in the programmed cell death pathway (PD-1/PD-L1). Because it is an oncoprotein associated with multiple cancer-related diseases, as well as a potential immunomodulator, controlling SHP2 activity is of significant therapeutic interest. Recently in our laboratories, a small molecule inhibitor of SHP2 was identified as an allosteric modulator that stabilizes the autoinhibited conformation of SHP2. A high throughput screen was performed to identify progressable chemical matter, and X-ray crystallography revealed the location of binding in a previously undisclosed allosteric binding pocket. Structure-based drug design was employed to optimize for SHP2 inhibition, and several new protein-ligand interactions were characterized. These studies culminated in the discovery of 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)pyrazin-2-amine (SHP099, 1), a potent, selective, orally bioavailable, and efficacious SHP2 inhibitor.

[Clinical research of modified taohe chengqi granule combined mannitol for treating complicated edema in affected limbs of patients after tibiofibulas double fracture operation].

OBJECTIVE: To observe the therapeutic efficacy of Modified Taohe Chengqi Granule (MTCG) combined mannitol for treating complicated edema in affected limbs of patients after tibiofibulas double fracture operation (TDFO). METHODS: Totally 64 TDFO patients complicated edema were randomly assigned to the treated group and the control group, 32 in each group. Those in the treated group took MTCG combined intravenous dripping of mannitol, while those in the control group received intravenous dripping of mannitol alone. The treatment course was 1 week. The clinical efficacy, the onset time, the swelling degree, and the pain index were observed and compared between the two groups. RESULTS: One week after operation, the effective rate was 98.0% and the markedly effective rate was 87.5% in the treated group, while they were 78.0% and 56.9% respectively in the control group. Better results were obtained in the treated group, showing statistical difference when compared with the control group (P < 0.05). As for the onset time for swelling subsiding, it was (2.4 +/- 1.3) days in the treated group and (3.8 +/- 2.9) days in the control group. There was statistical difference between the two groups (P < 0.05). Better effects on the swelling subsiding degree and the pain index were obtained in the treated group, showing statistical difference when compared with the control group (P < 0.05). CONCLUSIONS: MTCG combined mannitol could obviously abate the edema in affected limbs of patients after TDFO. It was a better treatment method for managing edema in the peri-operative period of orthopedics.

Clinical significance of microRNA-93 downregulation in human colon cancer.

AIM: MicroRNA-93 (miR-93) has been shown to suppress proliferation and colony formation of colon cancer stem cells. The aim of this study was to examine the expression pattern and prognostic value of miR-93 in patients with colon cancer. MATERIALS AND METHODS: A quantitative real-time PCR analysis was carried out to detect the expression levels of miR-93 in 138 paired samples of tumoral and nontumoral colon tissues diagnosed with colon cancer. Associations of miR-93 expression with clinicopathological parameters and survival were also examined. RESULTS: miR-93 expression was significantly decreased in tumoral compared with nontumoral colon tissues (P<0.001). Low miR-93 expression was significantly correlated with advanced tumor stage (P=0.02), positive nodal metastasis (P=0.006), and positive distant metastases (P=0.01). In addition, Kaplan-Meier survival analysis by Cox regression showed that low miR-93 expression [hazard ratio (HR), 10.2; 95% confidence interval (CI), 1.9-42.8, P=0.003] was associated closely with poor overall survival in patients with colon cancer. Moreover, multivariate analysis showed that miR-93 decreased expression (HR, 4.3; 95% CI, 0.8-17.2, P=0.02), advanced tumor stage (HR, 3.1; 95% CI, 0.2-13.9, P=0.04), positive nodal metastasis (HR, 4.1; 95% CI, 0.7-16.8, P=0.02), and positive distant metastases (HR, 3.7; 95% CI, 0.5-14.1, P=0.03) were independent risk factors for overall survival in patients with colon cancer. CONCLUSION: Our data show for the first time that the downregulation of miR-93 was significantly correlated with unfavorable clinicopathologic features and short overall survival in patients with colon cancer, suggesting that decreased expression of miR-93 be used as a novel prognostic factor for this disease.

Rethinking molecular similarity: comparing compounds on the basis of biological activity.

Since the advent of high-throughput screening (HTS), there has been an urgent need for methods that facilitate the interrogation of large-scale chemical biology data to build a mode of action (MoA) hypothesis. This can be done either prior to the HTS by subset design of compounds with known MoA or post HTS by data annotation and mining. To enable this process, we developed a tool that compares compounds solely on the basis of their bioactivity: the chemical biological descriptor "high-throughput screening fingerprint" (HTS-FP). In the current embodiment, data are aggregated from 195 biochemical and cell-based assays developed at Novartis and can be used to identify bioactivity relationships among the in-house collection comprising ~1.5 million compounds. We demonstrate the value of the HTS-FP for virtual screening and in particular scaffold hopping. HTS-FP outperforms state of the art methods in several aspects, retrieving bioactive compounds with remarkable chemical dissimilarity to a probe structure. We also apply HTS-FP for the design of screening subsets in HTS. Using retrospective data, we show that a biodiverse selection of plates performs significantly better than a chemically diverse selection of plates, both in terms of number of hits and diversity of chemotypes retrieved. This is also true in the case of hit expansion predictions using HTS-FP similarity. Sets of compounds clustered with HTS-FP are biologically meaningful, in the sense that these clusters enrich for genes and gene ontology (GO) terms, showing that compounds that are bioactively similar also tend to target proteins that operate together in the cell. HTS-FP are valuable not only because of their predictive power but mainly because they relate compounds solely on the basis of bioactivity, harnessing the accumulated knowledge of a high-throughput screening facility toward the understanding of how compounds interact with the proteome.

Tumor associated glycoprotein-72 is a novel marker for poor survival in hepatocellular carcinoma.

To investigate the relationship of tumor associated glycoprotein-72 (TAG-72) expression with clinicopathological features in hepatocellular carcinoma (HCC) patients. Sixty pairs of HCC and paracarcinomatous (PCLT) tissues, and 10 normal liver (NL) tissues were collected for Western blot analysis, and 244 pairs of HCC and PCLT tissues were collected for immunohistochemistry analysis. TAG-72 protein expression was elevated significantly in HCC tissues compared with PCLT and NL tissues. Its increased expression was correlated with TNM stage, Edmondson-Steiner grade, vein invasion and multiple tumor nodes. It is noteworthy that the HCC patients with high TAG-72 expression had shorter overall survival and disease-free survival than the patients with low expression. Multivariate Cox regression analysis revealed that TAG-72 expression was an independent prognostic factor for HCC patients. The current study demonstrated for the first time that the increased expression of TAG-72 was correlated with poor survival in patients with HCC, indicating that TAG-72 is a novel prognostic marker for HCC.

[Outcomes of surgeries for acute cervical spinal cord injury without cervical spine fracture or dislocation in young and middle-aged patients].

OBJECTIVE: To study the outcomes of surgeries for acute central cervical spinal cord injury without cervical spine fracture or dislocation in young and middle-aged patients. METHODS: The clinical data of 58 young and middle-aged patients with acute central cervical spinal cord injury treated in our hospital between August 2005 and August 2009 were analyzed retrospectively. Of these patients, 33 (24 males and 9 females) received surgical treatment and 25 (17 males and 8 females) had conservative therapy. The ASIA grade and ASIA motor and sensory score were used for evaluation at admission and at 14 days and 1 year after the treatment. The neurological symptoms and treatment outcomes in the two groups were evaluated. RESULTS: The proportion of patients with ASIA grade D-E and the ASIA motor and sensory scores were all significantly higher in the surgical group than in the non-surgical treatment group (P<0.05). CONCLUSION: For young and middle-aged patients with central cervical spinal cord injury, immediate surgery can relieve the pressure on the injured spinal cord and improve the micro-circulation to promote functional recovery of the spinal cord.

A lead discovery strategy driven by a comprehensive analysis of proteases in the peptide substrate space.

We present here a comprehensive analysis of proteases in the peptide substrate space and demonstrate its applicability for lead discovery. Aligned octapeptide substrates of 498 proteases taken from the MEROPS peptidase database were used for the in silico analysis. A multiple-category naïve Bayes model, trained on the two-dimensional chemical features of the substrates, was able to classify the substrates of 365 (73%) proteases and elucidate statistically significant chemical features for each of their specific substrate positions. The positional awareness of the method allows us to identify the most similar substrate positions between proteases. Our analysis reveals that proteases from different families, based on the traditional classification (aspartic, cysteine, serine, and metallo), could have substrates that differ at the cleavage site (P1-P1') but are similar away from it. Caspase-3 (cysteine protease) and granzyme B (serine protease) are previously known examples of cross-family neighbors identified by this method. To assess whether peptide substrate similarity between unrelated proteases could reliably translate into the discovery of low molecular weight synthetic inhibitors, a lead discovery strategy was tested on two other cross-family neighbors--namely cathepsin L2 and matrix metallo proteinase 9, and calpain 1 and pepsin A. For both these pairs, a naïve Bayes classifier model trained on inhibitors of one protease could successfully enrich those of its neighbor from a different family and vice versa, indicating that this approach could be prospectively applied to lead discovery for a novel protease target with no known synthetic inhibitors.

Which aspects of HTS are empirically correlated with downstream success?

High-throughput screening (HTS) is a well-established hit-finding approach used in the pharmaceutical industry. In this article, recent experience at Novartis with respect to factors influencing the success of HTS campaigns is discussed. An inherent measure of HTS quality could be defined by the assay Z and Z' factors, the number of hits and their biological potencies; however, such measures of quality do not always correlate with the advancement of hits to the later stages of drug discovery. Also, for many target classes, such as kinases, it is easy to identify hits, but, as a result of selectivity, intellectual property and other issues, the projects do not result in lead declarations. In this article, HTS success is defined as the fraction of HTS campaigns that advance into the later stages of drug discovery, and the major influencing factors are examined. Interestingly, screening compounds in individual wells or in mixtures did not have a major impact on the HTS success and, equally interesting, there was no difference in the progression rates of biochemical and cell-based assays. Particular target types, assay technologies, structure-activity relationships and powder availability had a much greater impact on success as defined above. In addition, significant mutual dependencies can be observed - while one assay format works well with one target type, this situation might be completely reversed for a combination of the same readout technology with a different target type. The results and opinions presented here should be regarded as groundwork, and a plethora of factors that influence the fate of a project, such as biophysical measurements, chemical attractiveness of the hits, strategic reasons and safety pharmacology, are not covered here. Nonetheless, it is hoped that this information will be used industry-wide to improve success rates in terms of hits progressing into exploratory chemistry and beyond. The support that can be obtained from new in silico approaches to phase transitions are also described, along with the gaps they are designed to fill.

[Infection of intervertebral space and the interventional therapy].

OBJECTIVE: To investigate the effect of interventional therapy in the treatment of intervertebral space infection. METHODS: The needle was punctured into the infected intervertebral space from the post-lateral side of the spine monitored by X-rays. The pus was drained, the degenerative disc tissues and necrosis tissues were excised and taken out, and at the end a drainaging catheter was put into the space through the needle. The patient should lie in bed absolutely. The antibiotics was injected into the space through the silicon catheter every day. Three to four weeks later, the catheter was removed. RESULTS: All the 8 patients got good results after the therapy. The low back pain was dramatically alleviated instantly at the day of operation. Erythrocyte sedimental rate gradually descended. After 3 approximately 4 weeks of treatment,the catheter was removed. CONCLUSION: Interventional therapy of the intervertebral space infection has notable advantage over the open operation.

One-stage surgical management for multilevel tuberculous spondylitis of the upper thoracic region by anterior decompression, strut autografting, posterior instrumentation, and fusion.

STUDY DESIGN: A retrospective clinical study of 1-stage surgical management for multilevel tuberculous spondylitis of the upper thoracic region (MTSUTR). OBJECTIVE: MTSUTR has rarely been documented in the literature. We present a retrospective clinical study of 23 patients with MTSUTR treated by anterior decompression, strut autografting, posterior instrumentation, and fusion. The purpose was to determine the clinical efficacy of such surgical treatment for MTSUTR. SUMMARY OF BACKGROUND DATA: It is considered safe and effective to treat surgically tuberculous spondylitis with local spinal cord compression. Many reports have documented a good clinical efficacy of surgical management for spinal tuberculosis. However, how to deal with MTSUTR is rarely reported in the literature. METHODS: There were 14 men and 9 women, with average age of 35 years. All patients underwent 1 stage anterior debridement, strut autografting, and posterior instrumentation and received combined medication antituberculosis chemotherapy for 12 to 24 months (average 18 mo). The following data were followed up for an average period of 42 months (24 to 60 mo) in these patients: deformity angle, neurologic function, and spinal bony fusion. RESULTS: The average preoperative deformity angle was 44 degrees, correcting to 20-degree postoperatively and 24 degrees at final follow up. In the series, 19 patients with preoperative neurologic deficit restored by 1.3 grades according to Frankel. All patients got bony spinal fusion within 6 months postoperatively. There was no recurrent tuberculous infection. CONCLUSIONS: Single-stage anterior debridement, strut autografting, posterior instrumentation, and fusion proved safe and effective for MTSUTR, which can achieve goals of complete spinal cord decompression and good deformity correction.

"Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection.

This work describes a novel semi-sequential technique for in silico enhancement of high-throughput screening (HTS) experiments now employed at Novartis. It is used in situations in which the size of the screen is limited by the readout (e.g., high-content screens) or the amount of reagents or tools (proteins or cells) available. By performing computational chemical diversity selection on a per plate basis (instead of a per compound basis), 25% of the 1,000,000-compound screening was optimized for general initial HTS. Statistical models are then generated from target-specific primary results (percentage inhibition data) to drive the cherry picking and testing from the entire collection. Using retrospective analysis of 11 HTS campaigns, the authors show that this method would have captured on average two thirds of the active compounds (IC(50) < 10 microM) and three fourths of the active Murcko scaffolds while decreasing screening expenditure by nearly 75%. This result is true for a wide variety of targets, including G-protein-coupled receptors, chemokine receptors, kinases, metalloproteinases, pathway screens, and protein-protein interactions. Unlike time-consuming "classic" sequential approaches that require multiple iterations of cherry picking, testing, and building statistical models, here individual compounds are cherry picked just once, based directly on primary screening data. Strikingly, the authors demonstrate that models built from primary data are as robust as models built from IC(50) data. This is true for all HTS campaigns analyzed, which represent a wide variety of target classes and assay types.

Flexible 3D pharmacophores as descriptors of dynamic biological space.

Development of a pharmacophore hypothesis related to small-molecule activity is pivotal to chemical optimization of a series, since it defines features beneficial or detrimental to activity. Although crystal structures may provide detailed 3D interaction information for one molecule with its receptor, docking a different ligand to that model often leads to unreliable results due to protein flexibility. Graham Richards' lab was one of the first groups to utilize "fuzzy" pattern recognition algorithms taken from the field of image processing to solve problems in protein modeling. Thus, descriptor "fuzziness" was partly able to emulate conformational flexibility of the target while simultaneously enhancing the speed of the search. In this work, we extend these developments to a ligand-based method for describing and aligning molecules in flexible chemical space termed FEature POint PharmacophoreS (FEPOPS), which allows exploration of dynamic biological space. We develop a novel, combinatorial algorithm for molecular comparisons and evaluate it using the WOMBAT dataset. The new approach shows superior retrospective virtual screening performance than earlier shape-based or charge-based algorithms. Additionally, we use target prediction to evaluate how FEPOPS alignments match the molecules biological activity by identifying the atoms and features that make the key contributions to overall chemical similarity. Overall, we find that FEPOPS are sufficiently fuzzy and flexible to find not only new ligand scaffolds, but also challenging molecules that occupy different conformational states of dynamic biological space as from induced fits.

Bridging chemical and biological space: "target fishing" using 2D and 3D molecular descriptors.

Bridging chemical and biological space is the key to drug discovery and development. Typically, cheminformatics methods operate under the assumption that similar chemicals have similar biological activity. Ideally then, one could predict a drug's biological function(s) given only its chemical structure by similarity searching in libraries of compounds with known activities. In practice, effectively choosing a similarity metric is case dependent. This work compares both 2D and 3D chemical descriptors as tools for predicting the biological targets of ligand probes, on the basis of their similarity to reference molecules in a 46,000 compound, biologically annotated chemical database. Overall, we found that the 2D methods employed here outperform the 3D (88% vs 67% success) in correct target prediction. However, the 3D descriptors proved superior in cases of probes with low structural similarity to other compounds in the database (singletons). Additionally, the 3D method (FEPOPS) shows promise for providing pharmacophoric alignment of the small molecules' chemical features consistent with those seen in experimental ligand/ receptor complexes. These results suggest that querying annotated chemical databases with a systematic combination of both 2D and 3D descriptors will prove more effective than employing single methods.

"Bayes affinity fingerprints" improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept?

Conventional similarity searching of molecules compares single (or multiple) active query structures to each other in a relative framework, by means of a structural descriptor and a similarity measure. While this often works well, depending on the target, we show here that retrieval rates can be improved considerably by incorporating an external framework describing ligand bioactivity space for comparisons ("Bayes affinity fingerprints"). Structures are described by Bayes scores for a ligand panel comprising about 1000 activity classes extracted from the WOMBAT database. The comparison of structures is performed via the Pearson correlation coefficient of activity classes, that is, the order in which two structures are similar to the panel activity classes. Compound retrieval on a recently published data set could be improved by as much as 24% relative (9% absolute). Knowledge about the shape of the "bioactive chemical universe" is thus beneficial to identifying similar bioactivities. Principal component analysis was employed to further analyze activity space with the objective to define orthogonal ligand bioactive chemical space, leading to nine major (roughly orthogonal) activity axes. Employing only those nine activity classes, retrieval rates are still comparable to original Bayes affinity fingerprints; thus, the concept of orthogonal bioactive ligand chemical space was validated as being an information-rich but low-dimensional representation of bioactivity space. Correlations between activity classes are a major determinant to gauge whether the desired multitarget activity of drugs is (on the basis of current knowledge) a feasible concept because it measures the extent to which activities can be optimized independently, or only by strongly influencing one another.