生物信息学在药物设计中的应用

生物信息学的飞速发展为药物开发提供了新的手段,计算机辅助药物设计是多学科交叉发展的产物。结合近些年来的一些成功实例,对数据库搜寻、计算机直接生成(全新药物设计)和进一步优化等计算机辅助药物设计技术及相关重要算法软件的新进展做一综述。     

Glioma-Targeted Therapeutics: Computer-Aided Drug Design Prospective

The Protein Journal - Amongst the several types of brain cancers known to humankind, glioma is one of the most severe and life-threatening types of cancer, comprising 40% of all primary brain...     

Colon-Targeted Oral Drug Delivery Systems: Design Trends and Approaches

Colon-specific drug delivery systems (CDDS) are desirable for the treatment of a range of local diseases such as ulcerative colitis, Crohn’s disease, irritable bowel syndrome, chronic pancreatitis, and colonic cancer. In addition, the colon can be a potential site for the systemic absorption of several drugs to treat non-colonic conditions. Drugs such as proteins and peptides that are known to degrade in the extreme gastric pH, if delivered to the colon intact, can be systemically absorbed by colonic mucosa. In order to achieve effective therapeutic outcomes, it is imperative that the designed delivery system specifically targets the drugs into the colon. Several formulation approaches have been explored in the development colon-targeted drug delivery systems. These approaches involve the use of formulation components that interact with one or more aspects of gastrointestinal (GI) physiology, such as the difference in the pH along the GI tract, the presence of colonic microflora, and enzymes, to achieve colon targeting. This article highlights the factors influencing colon-specific drug delivery and colonic bioavailability, and the limitations associated with CDDS. Further, the review provides a systematic discussion of various conventional, as well as relatively newer formulation approaches/technologies currently being utilized for the development of CDDS.KEY WORDS: colon targeting, factors affecting colon delivery, future trends, novel approaches, traditional approaches     

Towards Integrated Drug Substance and Drug Product Design for an Active Pharmaceutical Ingredient Using Particle Engineering

A novel experimental approach describing the integration of drug substance and drug production design using particle engineering techniques such as sonocrystallization, high shear wet milling (HSWM) and dry impact (hammer) milling were used to manufacture samples of an active pharmaceutical ingredient (API) with diverse particle size and size distributions. The API instability was addressed using particle engineering and through judicious selection of excipients to reduce degradation reactions. API produced using a conventional batch cooling crystallization process resulted in content uniformity issues. Hammer milling increased fine particle formation resulting in reduced content uniformity and increased degradation compared to sonocrystallized and HSWM API in the formulation. To ensure at least a 2-year shelf life based on predictions using an Accelerated Stability Assessment Program, this API should have a D [v, 0.1] of 55 μm and a D [v, 0.5] of 140 μm. The particle size of the chief excipient in the drug product formulation needed to be close to that of the API to avoid content uniformity and stability issues but large enough to reduce lactam formation. The novel methodology described here has potential for application to other APIs.     

膜窖的区室化调节功能及药物设计策略探讨

膜窖是脂筏的一种特殊类型,在哺乳动物的内皮细胞、脂肪细胞及平滑肌细胞质膜上分布尤为丰富。近年来对于膜窖的区室化调节与生理功能及其应用于药物设计方面的研究日益受到关注,如利用基因剔除、荧光共振能量转移等技术研究窖蛋白功能及膜窖内信号蛋白的互相作用,从而为新型药物的设计打下理论基础。     

Computer Aided Drug Design: Some Fundamental Aspects

Understanding the molecular basis of drug action and exploring the chemical interactions involved in the complex processes of drug delivery are among the most important goals of contemporary drug design. The major recent advances in the detailed, mechanistic interpretation of molecular interactions, the global and local shape analysis of electron density clouds making up the actual fuzzy bodies of molecules, novel similarity and complementary measures, the detailed and accurate computational visualization techniques of molecular level "Computational Microscopy", the advances in computer modeling of conformational processes and chemical reactions of drug molecules, the computer aided design of molecular templates fitting various receptor sites are among the powerful tools of computer aided drug discovery. In this contribution some of the latest advances are reviewed.     

Structure of Protein Interaction Networks and Their Implications on Drug Design

Protein-protein interaction networks (PINs) are rich sources of information that enable the network properties of biological systems to be understood. A study of the topological and statistical properties of budding yeast and human PINs revealed that they are scale-rich and configured as highly optimized tolerance (HOT) networks that are similar to the router-level topology of the Internet. This is different from claims that such networks are scale-free and configured through simple preferential-attachment processes. Further analysis revealed that there are extensive interconnections among middle-degree nodes that form the backbone of the networks. Degree distributions of essential genes, synthetic lethal genes, synthetic sick genes, and human drug-target genes indicate that there are advantageous drug targets among nodes with middle- to low-degree nodes. Such network properties provide the rationale for combinatorial drugs that target less prominent nodes to increase synergetic efficacy and create fewer side effects.     

基于膜上的酵母双杂交系统及其在药物开发中的应用

蛋白质是生命活动的基础.生物体内的蛋白质之间都存在着复杂的相互关系.由于蛋白质中的膜蛋白在各种各样重要细胞过程中起着关键的作用,如光合作用、呼吸作用、信号传导、免疫反应和营养物质的吸收等,因此越来越受到研究者们的重视.对膜蛋白的研究也越来越多.但因为膜蛋白具有疏水性,所以常常用传统的生物化学和遗传学方法,难以对膜蛋白之间以及膜蛋白与胞质蛋白之间的关系进行分析和鉴定.而传统的酵母双杂交系统又因其局限性,不能广泛地用于研究膜蛋白的相互作用.对研究膜蛋白之间及膜蛋白与胞质蛋白之间关系的一种有效方法—基于膜上的酵母双杂交系统,以及该方法在药物开发设计领域中的运用进行了介绍和综述.     

LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design

We have developed a new multi-purpose program, LigBuilder, for structure-based drug design. Within the structural constraints of the target protein, LigBuilder builds up ligands step by step using a library of organic fragments. Various operations, such as growing, linking, and mutation, have been implemented to manipulate molecular structures. The user can choose either growing or linking strategies for ligand construction and a genetic algorithm is adopted to control the whole construction process. Binding affinities of the ligands are estimated by an empirical scoring function and the bioavailabilities are evaluated by a set of chemical rules. Using thrombin and dihydrofolate reductase as examples, we have demonstrated that LigBuilder is able to generate chemical structures similar to the known ligands.     

Vinyl Sulfones as Antiparasitic Agents and a Structural Basis for Drug Design

Cysteine proteases of the papain superfamily are implicated in a number of cellular processes and are important virulence factors in the pathogenesis of parasitic disease. These enzymes have therefore emerged as promising targets for antiparasitic drugs. We report the crystal structures of three major parasite cysteine proteases, cruzain, falcipain-3, and the first reported structure of rhodesain, in complex with a class of potent, small molecule, cysteine protease inhibitors, the vinyl sulfones. These data, in conjunction with comparative inhibition kinetics, provide insight into the molecular mechanisms that drive cysteine protease inhibition by vinyl sulfones, the binding specificity of these important proteases and the potential of vinyl sulfones as antiparasitic drugs.Sleeping sickness (African trypanosomiasis), caused by Trypanosoma brucei, and malaria, caused by Plasmodium falciparum, are significant, parasitic diseases of sub-Saharan Africa (1). Chagas'' disease (South American trypanosomiasis), caused by Trypanosoma cruzi, affects approximately, 16–18 million people in South and Central America. For all three of these protozoan diseases, resistance and toxicity to current therapies makes treatment increasingly problematic, and thus the development of new drugs is an important priority (2–4).T. cruzi, T. brucei, and P. falciparum produce an array of potential target enzymes implicated in pathogenesis and host cell invasion, including a number of essential and closely related papain-family cysteine proteases (5, 6). Inhibitors of cruzain and rhodesain, major cathepsin L-like papain-family cysteine proteases of T. cruzi and T. brucei rhodesiense (7–10) display considerable antitrypanosomal activity (11, 12), and some classes have been shown to cure T. cruzi infection in mouse models (11, 13, 14).In P. falciparum, the papain-family cysteine proteases falcipain-2 (FP-2)⁶ and falcipain-3 (FP-3) are known to catalyze the proteolysis of host hemoglobin, a process that is essential for the development of erythrocytic parasites (15–17). Specific inhibitors, targeted to both enzymes, display antiplasmodial activity (18). However, although the abnormal phenotype of FP-2 knock-outs is “rescued” during later stages of trophozoite development (17), FP-3 has proved recalcitrant to gene knock-out (16) suggesting a critical function for this enzyme and underscoring its potential as a drug target.Sequence analyses and substrate profiling identify cruzain, rhodesain, and FP-3 as cathepsin L-like, and several studies describe classes of small molecule inhibitors that target multiple cathepsin L-like cysteine proteases, some with overlapping antiparasitic activity (19–22). Among these small molecules, vinyl sulfones have been shown to be effective inhibitors of a number of papain family-like cysteine proteases (19, 23–27). Vinyl sulfones have many desirable attributes, including selectivity for cysteine proteases over serine proteases, stable inactivation of the target enzyme, and relative inertness in the absence of the protease target active site (25). This class has also been shown to have desirable pharmacokinetic and safety profiles in rodents, dogs, and primates (28, 29). We have determined the crystal structures of cruzain, rhodesain, and FP-3 bound to vinyl sulfone inhibitors and performed inhibition kinetics for each enzyme. Our results highlight key areas of interaction between proteases and inhibitors. These results help validate the vinyl sulfones as a class of antiparasitic drugs and provide structural insights to facilitate the design or modification of other small molecule inhibitor scaffolds.     

Immunophilins and HIV-1 V3 Loop For Structure-Based Anti-AIDS Drug Design

Abstract

The model of the structural complex of cyclophilin A (CycA) belonging to the immunophilins family with the HIV-MN gpl20 V3 loop was generated, and the computer-aided design of the immunophilin-derived peptide able to mask the biologically crucial V3 segments was implemented.

To this end, the following problems were solved: (i) the NMR-based conformational analysis of the HIV-MN V3 loop was put into effect, and its low energy structure fitting the input experimental observations was determined; (ii) molecular docking of this V3 structure with the X-ray conformation of CycA was carried out, and the energy refining the simulated structural complex was performed; (iii) the matrix of inter-atomic distances for the amino acids of the molecules forming part of the built over-molecular ensemble was computed, the types of interactions responsible for its stabilization were analyzed, and the CycA stretch, which accounts for the binding to V3, was identified; (iv) the most probable 3D structure for this stretch in the unbound state was predicted, and its collation with the X-ray structure for the corresponding site of CycA was performed; (v) the potential energy function and its constituents were studied for the structural complex generated by molecular docking of the V3 loop with the CycA peptide offering the virtual molecule that imitates the CycA segment, making a key contribution to the interactions of the native protein with the HIV-1 principal neutralizing determinant; (vi) as a result of the studies above, the designed molecule was shown to be capable of the efficacious blockading the functionally crucial V3 sites; and (vii) based on the joint analysis of the evidence obtained previously and in the present study, the composition of the peptide cocktail presenting the promising anti-AIDS pharmacological substance was developed.

The molecules simulated here by molecular modeling methods may become the first representatives of a new class of the chemical compounds (immunophilin-derived peptides) offering the looking-forward basic structures for the design of efficacious and safe antiviral agents.     

Molecular Modelling of Human DT-Diaphorase For Enzyme-Directed Bioreductive Drug Design

Abstract

The enzyme DT-Diaphorase (NAD(P)H:quinone acceptor oxidoreductase, EC 1.6.99.2.; DTD) has been recognised as a good target for enzyme-directed bioreductive drug development. This is due to elevated levels of enzyme activity in several human tumour types and its role in the bioreductive activation of several quinone-based anti-cancer drugs.

Bioreductive drugs are designed to exploit one of the features of solid tumours, namely tumour hypoxia. However, selectivity of bioreductive drugs is not only governed by oxygen levels, but also by the levels of the enzymes catalysing bioreductive activation, leading to the concept of “enzyme-directed bioreductive drug development” introduced by Workman and Walton in 1990. This concept requires the identification of tumours within a patient that have elevated levels of enzyme activity (enzyme profiling) and treating the patient with drugs activated by such enzymes. DTD has been singled out as a particularly good candidate for such targeting. In order to rationalise the design of drugs to target DTD, molecular modelling techniques have been employed.

The human DTD three-dimensional structure has been modelled with homology to the known rat DTD structure (about 85% identity) and the model refined using energy minimisation. Drug-binding orientations have been determined and molecular dynamics simulations performed. Using data from a series of quinone based compounds with a broad range of substrate specificity we examine drug-enzyme interactions and suggest how DTD substrate specificity might be further optimised.     

From G Protein-coupled Receptor Structure Resolution to Rational Drug Design

A number of recent technical solutions have led to significant advances in G protein-coupled receptor (GPCR) structural biology. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.     

Design of a Tumor Homing Cell-Penetrating Peptide for Drug Delivery

The major drawbacks with conventional cancer chemotherapy are the lack of satisfactory specificity towards tumor cells and poor antitumor activity. In order to improve these characteristics, chemotherapeutic drugs can be conjugated to targeting moieties e.g. to peptides with the ability to recognize cancer cells. We have previously reported that combining a tumor homing peptide with a cell-penetrating peptide yields a chimeric peptide with tumor cell specificity that can carry cargo molecules inside the cells. In the present study, we have used a linear breast tumor homing peptide, CREKA, in conjunction with a cell-penetrating peptide, pVEC. This new chimeric peptide, CREKA–pVEC, is more convenient to synthesize and moreover it is better in translocating cargo molecules inside cancer cells as compared to previously published PEGA–pVEC peptide. This study demonstrates that CREKA–pVEC is a suitable vehicle for targeted intracellular delivery of a DNA alkylating agent, chlorambucil, as the chlorambucil–peptide conjugate was substantially better at killing cancer cells in vitro than the anticancer drug alone.     

Commentary: Why Pharmaceutical Scientists in Early Drug Discovery Are Critical for Influencing the Design and Selection of Optimal Drug Candidates

This commentary reflects the collective view of pharmaceutical scientists from four different organizations with extensive experience in the field of drug discovery support. Herein, engaging discussion is presented on the current and future approaches for the selection of the most optimal and developable drug candidates. Over the past two decades, developability assessment programs have been implemented with the intention of improving physicochemical and metabolic properties. However, the complexity of both new drug targets and non-traditional drug candidates provides continuing challenges for developing formulations for optimal drug delivery. The need for more enabled technologies to deliver drug candidates has necessitated an even more active role for pharmaceutical scientists to influence many key molecular parameters during compound optimization and selection. This enhanced role begins at the early in vitro screening stages, where key learnings regarding the interplay of molecular structure and pharmaceutical property relationships can be derived. Performance of the drug candidates in formulations intended to support key in vivo studies provides important information on chemotype-formulation compatibility relationships. Structure modifications to support the selection of the solid form are also important to consider, and predictive in silico models are being rapidly developed in this area. Ultimately, the role of pharmaceutical scientists in drug discovery now extends beyond rapid solubility screening, early form assessment, and data delivery. This multidisciplinary role has evolved to include the practice of proactively taking part in the molecular design to better align solid form and formulation requirements to enhance developability potential.     

CNS Drug Design Based on Principles of Blood-Brain Barrier Transport

Abstract: Lipid-soluble small molecules with a molecular mass under a 400–600-Da threshold are transported readily through the blood-brain barrier in vivo owing to lipid-mediated transport. However, other small molecules lacking these particular molecular properties, antisense drugs, and peptide-based pharmaceuticals generally undergo negligible transport through the blood-brain barrier in pharmacologically significant amounts. Therefore, if present day CNS drug discovery programs are to avoid termination caused by negligible blood-brain barrier transport, it is important to merge CNS drug discovery and CNS drug delivery as early as possible in the overall CNS drug development process. Strategies for special formulation that enable drug transport through the blood-brain barrier arise from knowledge of the molecular and cellular biology of blood-brain barrier transport processes.