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Computational design methods provide opportunities to discover novel and diverse designs that traditional optimization approaches cannot find or that use physical phenomena in ways that engineers have overlooked. However, existing methods require supervised objectives to search or optimize for explicit behaviors or functions — e.g., optimizing aerodynamic lift. In contrast, this paper unpacks what it means to discover interesting behaviors or functions we do not know about a priori using data from experiments or simulation in a fully unsupervised way. Doing so enables computers to invent or re-invent new or existing mechanical functions given only measurements of physical fields (e.g., pressure or electromagnetic fields) without directly specifying a set of objectives to optimize. This paper explores this approach via two related parts. First, we study clustering algorithms that can detect novel device families from simulation data. Specifically, we contribute a modification to the Hierarchical Density-Based Spatial Clustering of Applications with Noise algorithm via the use of the silhouette score to reduce excessively granular clusters. Second, we study multiple ways by which we preprocess simulation data to increase its discriminatory power in the context of clustering device behavior. This leads to an insight regarding the important role that a design’s representation has in compactly encoding its behavior. We test our contributions via the task of discovering designs that function as fluidic logic gates. We generate synthetic data that mimics fluidic devices and show that our proposed contributions better discover logic gates, as measured by adjusted Rand score. Specifically, combining our Resolution Selection preprocessing and principal component analysis resulted in the highest and tightest spread of adjusted Rand scores on our tested datasets. This opens up new avenues of research wherein computers can automatically explore different types of physics and then derive new device functions, behaviors, and structures without the need for human labels or guidance.

Freeze-drying, also known as lyophilization, is a dehydration process designed to prolong the shelf life of injectable drug products. Here, we provide regulatory considerations for manufacturing processes specific to lyophilized injectable products. Specifically, a general discussion on each unit operation, including compounding, filtration, filling, and lyophilization, is provided to help the pharmaceutical industry establish reliable manufacturing processes from a regulatory perspective. In addition, a list of manufacturing-related deficiencies identified from a total of 263 new drug applications (NDAs) and abbreviated new drug applications (ANDAs) submitted for lyophilized injectable products is provided. We hope that the information presented in this report may help applicants avoid some common manufacturing-related deficiencies in regulatory submissions, thereby making high-quality lyophilized pharmaceuticals expeditiously available to the American public.

Die Entstehung von Arzneimittelresistenzen ist eines der grundlegenden Probleme der Medizin. Dass sich bei HIV/AIDS so schnell resistente HIV-1-Varianten einstellen, ist ein groses Hindernis fur die modernen Therapien. Wichtige Zielmolekule der derzeitigen antiretroviralen Therapien sind Inhibitoren der HIV-1-Protease. Das Virus entwickelt Resistenzen, wenn Mutationen die Inhibitorbindung des Enzyms verandern und somit die Effizienz mindern. Um diese Resistenzbildung zu vermeiden, haben wir Inhibitoren erforscht, die am aktiven Zentrum der Protease Wasserstoffbrucken zum Proteinruckgrat bilden. Weil sich die Geometrie am katalytischen Zentrum ohne Funktionsverlust nicht andern kann, schranken solche Wechselwirkungen die Moglichkeiten der Protease zur Resistenzbildung erheblich ein. Hier diskutieren wir das enzymatische Strukturprinzip, auf dem unser Konzept der Ruckgratbindung beruht. Besonderes Augenmerk richten wir auf die Anwendung des Konzepts in unseren jungeren Arbeiten zu antiviralen Inhibitoren der HIV-1-Protease.

Over the past two decades, HIV protease inhibitors have helped revolutionize the treatment of HIV/AIDS transforming this deadly ailment into a more manageable chronic infection. Due to intensive research in the area, a variety of protease inhibitors are now commercially available each of which possesses distinct characteristics and a unique tale of discovery. This manuscript reviews the design and development of the 10 currently available protease inhibitors saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, lopinavir, atazanavir, fosamprenavir, tipranavir, and darunavir. Special attention is given to the research efforts leading to their discovery and the successes and limitations of these drugs in the clinics. A brief review of the biology associated with the HIV-1 protease target is provided in addition to a discussion of novel drug candidates currently under investigation. Keywords: Agenerase; amprenavir; Aptivus; atazanavir; Crixivan; darunavir; fosamprenavir; HIV protease; indinavir; Invirase; Kaletra; lopinavir; nelfinavir; Norvir; Prezista; protease inhibitor; Reyataz; ritonavir; saquinavir; tipranavir; Viracept

The structure-based design, synthesis, and biological evaluation of a series of nonpeptidic macrocyclic HIV protease inhibitors are described. The inhibitors are designed to effectively fill in the hydrophobic pocket in the S1'-S2' subsites and retain all major hydrogen bonding interactions with the protein backbone similar to darunavir (1) or inhibitor 2. The ring size, the effect of methyl substitution, and unsaturation within the macrocyclic ring structure were assessed. In general, cyclic inhibitors were significantly more potent than their acyclic homologues, saturated rings were less active than their unsaturated analogues and a preference for 10- and 13-membered macrocylic rings was revealed. The addition of methyl substituents resulted in a reduction of potency. Both inhibitors 14b and 14c exhibited marked enzyme inhibitory and antiviral activity, and they exerted potent activity against multidrug-resistant HIV-1 variants. Protein-ligand X-ray structures of inhibitors 2 and 14c provided critical molecular insights into the ligand-binding site interactions.

Structure-based design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors are described. In an effort to enhance interactions with protease backbone atoms, we have incorporated stereochemically defined methyl-2-pyrrolidinone and methyl oxazolidinone as the P1'-ligands. These ligands are designed to interact with Gly-27' carbonyl and Arg-8 side chain in the S1'-subsite of the HIV protease. We have investigated the potential of these ligands in combination with our previously developed bis-tetrahydrofuran (bis-THF) and cyclopentanyltetrahydrofuran (Cp-THF) as the P2-ligands. Inhibitor 19b with a (R)-aminomethyl-2-pyrrolidinone and a Cp-THF was shown to be the most potent compound. This inhibitor maintained near full potency against multi-PI-resistant clinical HIV-1 variants. A high resolution protein-ligand X-ray crystal structure of 19b-bound HIV-1 protease revealed that the P1'-pyrrolidinone heterocycle and the P2-Cp-ligand are involved in several critical interactions with the backbone atoms in the S1' and S2 subsites of HIV-1 protease.

A pilot-plant scale desymmetrization of the cyclic meso-epoxide 4b, using a chiral lithium amide prepared from symmetrical diamine 17, was designed and implemented to provide allylic alcohol 3b in high yield and greater than 99% ee. This chiral alcohol was converted to ketone 2b, a key intermediate in a new asymmetric synthesis of LY459477. Chiral diamine 17 was prepared from a readily available chiral precursor, (R)-α-methylbenzylamine, and could be recovered from the reaction mixture and reused. Studies performed to probe the mechanism of the rearrangement reaction of epoxide 4b showed that diamine 17 provided an optimal combination of selectivity and scaleability for this process.

This paper describes algorithms and software for decomposing CAD models for a new mold manufacturing process called WirePATH™, which uses wire electrical discharge machining (EDM) to reduce mold fabrication time. A decomposition strategy has been developed to account for the limitations of wire EDM. During decomposition, CAD models are separated into manufacturable segments and then layered if they contain curved or relatively flat sloped surfaces because wire EDM is limited to steeply sloped ruled surfaces. A new algorithm for direct adaptive layering of CAD models is developed. The algorithm analyzes surface error by comparing line segments against actual curves from the model surface. Also, the maximum angle needed to produce each layer is checked, and, in some cases, the layers are reconstructed to conform to the maximum angle.

The SAR at C-5 of the 10-methoxy-2,2,4-trimethylbenzopyrano[3,4-f]quinoline core leading to identification of (-) anti 1-methylcyclohexen-3-yl as the optimum substituent that imparts minimal GR mediated in vitro transcriptional activation while maintaining full transcriptional repression is described. The in vitro profile of these candidates in human cell assays relevant to the therapeutic window of glucocorticoid modulators is outlined.

Pladienolide B (PB) is a potent cancer cell growth inhibitor that targets the SF3B1 subunit of the spliceosome. There is considerable interest in the compound as a potential chemotherapeutic, as well as a tool to study SF3B1 function in splicing and cancer development. The molecular structure of PB, a bacterial natural product, contains a 12-member macrolide ring with an extended epoxide-containing side chain. Using a novel concise enantioselective synthesis, we created a series of PB structural analogs and the structurally related compound herboxidiene. We show that two methyl groups in the PB side chain, as well as a feature of the macrolide ring shared with herboxidiene, are required for splicing inhibition in vitro. Unexpectedly, we find that the epoxy group contributes only modestly to PB potency and is not absolutely necessary for activity. The orientations of at least two chiral centers off the macrolide ring have no effect on PB activity. Importantly, the ability of analogs to inhibit splicing in vitro directly correlated with their effects in a series of cellular assays. Those effects likely arise from inhibition of some, but not all, endogenous splicing events in cells, as previously reported for the structurally distinct SF3B1 inhibitor spliceostatin A. Together, our data support the idea that the impact of PB on cells is derived from its ability to impair the function of SF3B1 in splicing and also demonstrate that simplification of the PB scaffold is feasible.

The effect of quantified resistance and high impact exercise training on bone mass as modified by age and oral contraceptive (OCont) use in young women was studied.Women were categorized by age (18-23 vs 24-31 yr) and OCont use, and were then randomized into either three sessions of resistance exercise plus 60 min.wk-1 of jumping rope or a control group for 24 months. Total body, spine, femoral neck, greater trochanter, Ward's area, and radial bone mineral density (BMD) and/or content (BMC), biochemical markers of bone turnover, dietary intake of calcium, lean body mass, maximal oxygen uptake, and strength were determined at baseline and every 6 months.Total body (TB) BMC percent change from baseline was higher in exercisers compared with nonexercisers at 6 and 24 months. OCont users had lower bone turnover at baseline and a decrease in TBBMC from baseline compared with non-OCont users at 24 months. Spine BMC and BMD decreased in the exercise and OCont group at 6 months and remained significantly below nonexercisers who used oral contraceptives at 2 yr. Femoral neck BMD also decreased in the exercise and oral contraceptive group at 6 months.Exercise prevented a decline in TBBMC seen in the nonexercisers. On the other hand, exercise in oral contraceptive users prevented the increase observed in the spine of the nonexercise plus OCont group.

This paper discusses the past 25 years of research in feature recognition. Although a great variety of feature recognition techniques have been developed, the discussion here focuses on the more successful ones. These include graph based and “hint” based methods, convex hull decomposition, and volume decomposition-recomposition techniques. Recent advances in recognizing features with free form features are also presented. In order to benchmark these methods, a frame of reference is created based on topological generality, feature interactions handled, surface geometry supported, pattern matching criteria used, and computational complexity. This framework is used to compare each of the recognition techniques. Problems related to domain dependence and multiple interpretations are also addressed. Finally, some current research challenges are discussed.

Bioelectrical impedance analysis (BIA) is a convenient, inexpensive, and noninvasive technique for measuring body composition. BIA has been strongly correlated with total body water (TBW) and also has been validated against hydrodensitometry (HD). The accuracy and clinical utility of BIA and HD during periods of substantial weight loss remain controversial. We measured body composition in moderately and severely obese patients serially using both methods during a very-low-energy diet (VLED). Mean initial weight in these patients was 116 (+/-30) kg (range, 74-196 kg). Mean weight loss was 24 (+/-13) kg with a decrease in fat mass (FM) by HD of kg (p < 0.001) and a decrease in fat-free mass (FFM) of 3.6 kg (p < 0.05). Loss of FFM is best predicted by the rate (kg/wk) of weight loss (r2 = 0.86, p < 0.0001). FFM, as predicted from BIA equations, was highly correlated with FFM as estimated by HD during all testing sessions (r = 0.92-0.98). Although highly correlated, BIA overestimated FFM relative to HD and this difference appeared to be more pronounced for taller patients with greater truncal obesity. Although the discrepancy was no greater during weight-loss treatment, the level of disagreement was considerable. Therefore, the two methods cannot be used interchangeably to monitor relative changes in body composition in patients with obesity during treatment with VLED. The discrepancy between BIA and HD may be caused by body mass distribution considerations and by perturbations in TBW which affect the hydration quotient for FFM (BIA) and/or which affect the density constants for FFM and FM (HD).

Bone remodeling as a response to exercise in human subjects is described in the literature, although most studies treat exercise as a qualitative factor contributing to bone remodeling. Quantitative description requires assessment of the mechanical loads on the bones. This work describes a generalized lower extremity model that uses existing musculoskeletal modeling techniques to quantify mechanical variables in the femoral neck during exercise. An endurance exercise program consisting of walking, jogging jumping rope, and weight-training was analyzed. Peak femoral neck cortex stresses and strains were high during jogging and squatting, compared to walking, whereas jumping rope and other weight-training exercises produced peak stresses comparable to or lower than walking. Peak stress and strain rates were significantly higher for walking, jumping rope, and jogging than for weight-training. The model should prove useful for any study investigating a quantitative relationship between exercise and bone remodeling.

An enantioselective and convergent total synthesis of pladienolide B (1) is described. Pladienolide B binds to the SF3b complex of a spliceosome and inhibits mRNA splicing activity. The synthesis features an epoxide opening reaction, an asymmetric reduction of a β-keto ester, and a cross metathesis strategy for the side chain synthesis.

The structure-based design, synthesis, and X-ray structure of protein-ligand complexes of exceptionally potent and selective β-secretase inhibitors are described. The inhibitors are designed specifically to interact with S(1)' active site residues to provide selectivity over memapsin 1 and cathepsin D. Inhibitor 5 has exhibited exceedingly potent inhibitory activity (K(i) = 17 pM) and high selectivity over BACE 2 (>7000-fold) and cathepsin D (>250000-fold). A protein-ligand crystal structure revealed important molecular insight into these selectivities. These interactions may serve as an important guide to design selectivity over the physiologically important aspartic acid proteases.

The evolution of drug resistance is one of the most fundamental problems in medicine. In HIV/AIDS, the rapid emergence of drug-resistant HIV-1 variants is a major obstacle to current treatments. HIV-1 protease inhibitors are essential components of present antiretroviral therapies. However, with these protease inhibitors, resistance occurs through viral mutations that alter inhibitor binding, resulting in a loss of efficacy. This loss of potency has raised serious questions with regard to effective long-term antiretroviral therapy for HIV/AIDS. In this context, our research has focused on designing inhibitors that form extensive hydrogen-bonding interactions with the enzyme's backbone in the active site. In doing so, we limit the protease's ability to acquire drug resistance as the geometry of the catalytic site must be conserved to maintain functionality. In this Review, we examine the underlying principles of enzyme structure that support our backbone-binding concept as an effective means to combat drug resistance and highlight their application in our recent work on antiviral HIV-1 protease inhibitors.

HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005–2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.

The evolution of drug resistance is one of the most fundamental problems in medicine. In HIV/AIDS, the rapid emergence of drug‐resistant HIV‐1 variants is a major obstacle to current treatments. HIV‐1 protease inhibitors are essential components of present antiretroviral therapies. However, with these protease inhibitors, resistance occurs through viral mutations that alter inhibitor binding, resulting in a loss of efficacy. This loss of potency has raised serious questions with regard to effective long‐term antiretroviral therapy for HIV/AIDS. In this context, our research has focused on designing inhibitors that form extensive hydrogen‐bonding interactions with the enzyme’s backbone in the active site. In doing so, we limit the protease’s ability to acquire drug resistance as the geometry of the catalytic site must be conserved to maintain functionality. In this Review, we examine the underlying principles of enzyme structure that support our backbone‐binding concept as an effective means to combat drug resistance and highlight their application in our recent work on antiviral HIV‐1 protease inhibitors., Impeding the evolution of drug resistance: HIV protease inhibitors are critical to antiretroviral treatment regimens. However, the rapid onset of drug resistance limits the effectiveness of most approved inhibitors. The structure‐based design of inhibitors targeting atoms in the protein backbone is an attractive strategy for maintaining drug efficacy. This approach limits the enzyme's ability to evolve resistance without sacrificing its catalytic activity.WILEY-VCH

L-selectride reduction of a chiral or achiral enone followed by reaction of the resulting enolate with optically active alpha-alkoxy aldehydes proceeded with excellent diastereoselectivity. The resulting alpha,alpha-dimethyl-beta-hydroxy ketones are inherent to a variety of biologically active natural products.

L-selectride reduction of a chiral or achiral enone followed by reaction of the resulting enolate with optically active alpha-alkoxy aldehydes proceeded with excellent diastereoselectivity. The resulting alpha,alpha-dimethyl-beta-hydroxy ketones are inherent to a variety of biologically active natural products.

The D-Ala-D-Ala adding enzyme (MurF) from Streptococcus pneumoniae catalyzes the ATP-dependent formation of the UDP-MurNAc-pentapeptide, a critical component of the bacterial cell wall. MurF is a potential target for antibacterial design because it is unique to bacteria and performs an essential non-redundant function in the bacterial cell. The recent discovery and subsequent cocrystal structure determination of MurF in complex with a new class of inhibitors served as a catalyst to begin a medicinal chemistry program aimed at improving their potency. We report here a multidisciplinary approach to this effort that allowed for rapid generation of cocrystal structures, thereby providing the crystallographic information critical for driving the inhibitor optimization process. This effort resulted in the discovery of low-nanomolar inhibitors of this bacterial enzyme.

A novel class of MurF inhibitors was discovered and structure-activity relationship studies have led to several potent compounds with IC(50)=22 approximately 70 nM. Unfortunately, none of these potent MurF inhibitors exhibited significant antibacterial activity even in the presence of bacterial cell permeabilizers.

Recent developments in Computer Aided Design (CAD) have drastically reduced overall design cycle time and cost. In this paper, wirePATH, a new method for rapid direct tooling, is presented. By using specialized interactive segmentation computer software and wire electrical discharge machining (wire EDM), wirePATH can reduce manufacturing time and cost for injection molds, casting patterns, and dies. Compared to other conventional-mold making methods, wirePATH can reduce fabrication time by as much as 40 to 70%. Wirepath can use a combination of wire EDM and other processes. Our method provides a new means to produce a greater variety in products by changing only portions of the tooling. Segments allow a part of a mold to be replaced to accommodate design changes and repair. WirePATH enables new applications of wire EDM to more complex shapes by bridging the gaps between CAD, our method, wire EDM and conventional manufacturing processes.

The preparation and characterization of a series of selective glucocorticoid receptor modulators are described. The preliminary structure-activity relationship of nonaromatic C-5 substitution on the tetracyclic quinoline core showed a preference for small lipophilic side chains. Proper substitution at this position maintained the transcriptional repression of proinflammatory transcription factors while diminishing the transcriptional activation activity of the ligand/glucocorticoid receptor complex. The optimal compounds described in this study were the allyl analogue 18 and cyclopentyl analogue 32. These candidates showed slightly less potent, highly efficacious E-selectin repression with significantly reduced levels of glucocorticoid response element activation in reporter gene assays vs prednisolone. Allyl analogue 18 was evaluated in vivo. An oral dose of 18 showed an ED(50) = 1.7 mg/kg as compared to 1.2 mg/kg for prednisolone in the Sephadex-induced pulmonary eosinophilia model and an ED(50) = 15 mg/kg vs 4 mg/kg for prednisolone in the carrageenan-induced paw edema model.

Interaction between humans and support surfaces during landing involves prospective action as demonstrated by the activationofmusclespriortocontact.Onsetofmedialgastro~emiusactivityhasbeenfound oberel tiv ly consistent across surfaces varying in compliance, however, amplitude of activity has produced mixed results. This study examines the eff& of landing surface on the onset and amplitude of muscle activity of the soleus and gastrocnemius. Male recreational athletes (n=9) performed a series of nine drop landings (.72 m) onto each of two surfaces: force plates and composite landing mats (10 cm; 100 ILD). The reaction forces for each foot were quantified using two forceplates (800 Hz). Segment kinematics were recorded simultaneously using high speed film (100 fps). Activity of three lower extremity muscles (MG, SO, TA) prior to contact were monitored using surface electromyography (1800 Hz). Results indicate that the duration of muscle preactivation and amplitude of the SO tends to increase when landing on the force plates as compared to the mats; However, no significant differences in time of onset or amplitude were noted for the MG between surfaces (p-z.05). The difference in response by the MG and SO muscles may be a reflection of the differences in fiber type composition, architecture, and/or the number of joints crossed by each muscle.

Studies on quantitation of RNA synthesis in eucaryotic cells have frequently used adenosine as the radioactively labeled precursor, largely because of the convenience of the firefly luciferin-luciferase assay in measuring ATP pool specific activity (1,2). This could result in some difficulties if the addition of poly(A) to the 3′ OH end of RNA represents a significant portion of total incorporation, as is the case in sea-urchin embryos (3). In addition, in some cases, the ATP pool may be large enough to prevent the use of adenosine as an effective labeling agent. Hence, a simple and sensitive method for the determination of the specific activity of the other nucleic acid precursor pools would be of value. Although the crystalline luciferase is specific for ATP, extracts of firefly lanterns most commonly used for quantitating ATP (4–9) also exhibit activity with other ribonucleoside triphosphates, adenosine tetraphosphate, ADP, and the deoxyribonucleoside triphosphates. This activity is due to the presence of contaminating enzymes such as nucleoside 5′-diphosphate kinase and adenylate kinase which catalyze the formation of ATP from these nucleotides and trace amounts of ADP, also present in the extracts (10–13). Recently, Manandhar and Van Dyke (14) have reported a procedure for quantitating picomole levels of GTP with a crude extract of firefly lanterns. In the present study, we have adapted their procedure to develop an assay for GTP pool specific activity in Xenopus laevis oocytes microinjected with [8-3H]GTP. Our assay may be extended to the analysis of any nucleoside triphosphate pool, provided that an adequate chromatography system is available for the separation of the extracted nucleotides.

The role of photos in biographical study, especially of twentiethcentury American authors, has become increasingly important in recent years, particularly with the ready availability of the collections at Yale University, the University of California, and many other libraries. Unfortunately, however, there are many more accumulations in the possession of private individuals, collectors, and families that are not as accessible.