Incorporating protein flexibility into docking and structure-based drug design

The use of structure in drug design has become widespread, mainly thanks to recent advances in crystallography. Nevertheless, biological macromolecules are intrinsically flexible and it is increasingly evident that their function depends critically on both their structure and dynamics. In this review the authors discuss the implications of protein flexibility for drug design and review recent progress in incorporating protein flexibility into docking and structure-based drug design.     

From laptop to benchtop to bedside: structure-based drug design on protein targets

As an important aspect of computer-aided drug design, structure-based drug design brought a new horizon to pharmaceutical development. This in silico method permeates all aspects of drug discovery today, including lead identification, lead optimization, ADMET prediction and drug repurposing. Structure-based drug design has resulted in fruitful successes drug discovery targeting proteinligand and protein-protein interactions. Meanwhile, challenges, noted by low accuracy and combinatoric issues, may also cause failures. In this review, state-of-the-art techniques for protein modeling (e.g. structure prediction, modeling protein flexibility, etc.), hit identification/ optimization (e.g. molecular docking, focused library design, fragment-based design, molecular dynamic, etc.), and polypharmacology design will be discussed. We will explore how structure-based techniques can facilitate the drug discovery process and interplay with other experimental approaches.     

Targeting protein multiple conformations: a structure-based strategy for kinase drug design

Multiple conformations of a protein kinase target offer an opportunity to design small-molecule inhibitors with distinct but clinically useful profiles. This article analyzes and classifies the binding pockets in the kinase catalytic cleft in different conformational states. Targeting kinase multiple conformations as an emerging strategy in the field is exemplified with important small-molecule agents in the clinic. The structure-based analysis in the paper provides a rationale for thwarting the development of drug-resistant mutations in antikinase therapy.     

Challenges and opportunities for new protein crystallization strategies in structure-based drug design

Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process, while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high-resolution (< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate. The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.     

Challenges and opportunities for new protein crystallization strategies in structure-based drug design

Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 ?) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.     

Structural genomics: bridging functional genomics and structure-based drug design

Considerable advances in structural genomics have been witnessed in the last year. Several pilot studies have begun to report their initial results, and new centers have been funded to join the endeavor. The legacies of the genome sequencing efforts, namely high-throughput molecular biology and whole-organism genome sequences, have been integrated as front-end modules for structural genomics pipelines. Impressive advances have been made in NMR spectroscopy and X-ray crystallography. New methods in structural bioinformatics and computational chemistry have been published that provide the means to exploit the wealth of new information in drug discovery. Not surprisingly, the biopharmaceutical industry has been quick to recognize the benefits of these new developments and has begun to adopt them. This article reviews recent results from structural genomics initiatives and the potential applications of new information and technologies in the drug discovery process.     

From DNA to NDA--the impact of recombinant DNA technology on new drug development

Man's long-standing efforts to alter living things through genetic manipulation have become reality. Recent advances in recombinant DNA technology have the potential to alter the drug-development process profoundly. The pharmaceutical industry has had to adjust its research efforts and develop new state-of-the-art laboratories. In addition to the standard biological and in vivo assays, many new tests are required, e.g., amino acid sequencing, high-pressure liquid chromatography, and radioimmunoassays. Academic researchers have played a vital role in developing the new biotechnology, supplying most of the basic scientific knowledge and the initial supply of the scientific work force. The recent shifting of support for scientific training from the government to the pharmaceutical industry has resulted in unprecedented academe-industry relationships. Universities now stand to profit significantly from patent rights resulting from biotechnology research efforts. While the advances in biotechnology have had considerable impact on the pharmaceutical industry and academia, they have thus far had only a minor impact on the regulatory process. To date, the preferred regulatory path appears to be modification of existing procedures through the issuance of guidelines, which can be updated as knowledge increases.     

Latest developments in crystallography and structure-based design of protein kinase inhibitors as drug candidates

Protein kinases have been identified as being implicated in many diseases, and the launch of the anti-cancer Bcr/Abl-kinase inhibitor Glivec has been a major advance in validating protein kinases as 'druggable' targets. High-resolution data exists for many classes of protein kinases and, in some cases, these structures are co-complexed with an inhibitor and/or substrate mimic. Coupled with the increasing reliability of computational predictions, structure-based design is now playing an increasingly important role in the discovery and optimisation of novel, potent and selective protein kinase inhibitors.     

De novo drug design: integration of structure-based and ligand-based methods

Structure-based and ligand-based methods are used to derive predictive models in de novo drug design. Structure-based methods rely exclusively on prior knowledge of a protein structure to derive novel ligands, while ligand-based methods are traditionally used when no protein structure is available. Where there is sufficient information, these methods can be used in conjunction to increase the accuracy of simulation and enhance the drug design process. This review presents developments in the integration of these methods for de novo drug design, and recent results from both systems are highlighted.     

Biotechnology and genetic engineering in the new drug development. Part I. DNA technology and recombinant proteins

Pharmaceutical biotechnology has a long tradition and is rooted in the last century, first exemplified by penicillin and streptomycin as low molecular weight biosynthetic compounds. Today, pharmaceutical biotechnology still has its fundamentals in fermentation and bioprocessing, but the paradigmatic change affected by biotechnology and pharmaceutical sciences has led to an updated definition. The biotechnology revolution redrew the research, development, production and even marketing processes of drugs. Powerful new instruments and biotechnology related scientific disciplines (genomics, proteomics) make it possible to examine and exploit the behavior of proteins and molecules.Recombinant DNA(rDNA) technologies (genetic, protein, and metabolic engineering) allow the production of a wide range of peptides, proteins, and biochemicals from naturally nonproducing cells. This technology, now approximately 25 years old, is becoming one of the most important technologies developed in the 20^th century.Pharmaceutical products and industrial enzymes were the first biotech products on the world market made by means of rDNA. Despite important advances regarding rDNA applications in mammalian cells, yeasts still represent attractive hosts for the production of heterologous proteins. In this review we describe these processes.     

Free energy component analysis for drug design: a case study of HIV-1 protease-inhibitor binding.

A theoretically rigorous and computationally tractable methodology for the prediction of the free energies of binding of protein-ligand complexes is presented. The method formulated involves developing molecular dynamics trajectories of the enzyme, the inhibitor, and the complex, followed by a free energy component analysis that conveys information on the physicochemical forces driving the protein-ligand complex formation and enables an elucidation of drug design principles for a given receptor from a thermodynamic perspective. The complexes of HIV-1 protease with two peptidomimetic inhibitors were taken as illustrative cases. Four-nanosecond-level all-atom molecular dynamics simulations using explicit solvent without any restraints were carried out on the protease-inhibitor complexes and the free proteases, and the trajectories were analyzed via a thermodynamic cycle to calculate the binding free energies. The computed free energies were seen to be in good accord with the reported data. It was noted that the net van der Waals and hydrophobic contributions were favorable to binding while the net electrostatics, entropies, and adaptation expense were unfavorable in these protease-inhibitor complexes. The hydrogen bond between the CH2OH group of the inhibitor at the scissile position and the catalytic aspartate was found to be favorable to binding. Various implicit solvent models were also considered and their shortcomings discussed. In addition, some plausible modifications to the inhibitor residues were attempted, which led to better binding affinities. The generality of the method and the transferability of the protocol with essentially no changes to any other protein-ligand system are emphasized.     

Targeting mitogen-activated protein kinase phosphatase-1 (MKP-1): structure-based design of MKP-1 inhibitors and upregulators

Mitogen-activated protein kinase phosphatases (MKPs) are dual specificity protein phosphatases (DUSPs) that dephosphorylate both phospho-tyrosine and phospho-threonine residues on mitogen-activated protein kinases (MAPKs). Because the MAPK family of signalling molecules (phospho-p38 MAPK, c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK)) play essential roles in cell signalling pathways that regulate cell growth and inflammation, controlling MAPK-mediated pathways is a therapeutically attractive strategy. While small molecule MAPK inhibitors have utility, in this review we will focus on exploring the potential of targeting the endogenous MAPK deactivator--MKP-1. Importantly, there is a strong justification for developing both inhibitors and upregulators of MKP-1 because of the diverse roles played by MAPKs in disease: for example, in cancer, MKP-1 inhibitors may prove beneficial, as MKP-1 is overexpressed and is considered responsible for the failure of JNK-driven apoptotic pathways induced by chemotherapeutics; conversely, in inflammatory diseases such as asthma and arthritis, MKP-1 reduces MAPK-mediated signalling and developing novel ligands to upregulate MKP-1 levels would be a therapeutically attractive anti-inflammatory strategy. Thus, in this review we utilise MKP-1 homology modeling to highlight the structural features of MKP-1 inhibitors that permit potent and selective inhibition, and to provide insights into the structural requirements for selective MKP-1 upregulators.     

Use of structure-based drug design approaches to obtain novel anthranilic acid acyl carrier protein synthase inhibitors

Acyl carrier protein synthase (AcpS) catalyzes the transfer of the 4'-phosphopantetheinyl group from the coenzyme A to a serine residue in acyl carrier protein (ACP), thereby activating ACP, an important step in cell wall biosynthesis. The structure-based design of novel anthranilic acid inhibitors of AcpS, a potential antibacterial target, is presented. An initial high-throughput screening lead and numerous analogues were modeled into the available AcpS X-ray structure, opportunities for synthetic modification were identified, and an iterative process of synthetic modification, X-ray complex structure determination with AcpS, biological testing, and further modeling ultimately led to potent inhibitors of the enzyme. Four X-ray complex structures of representative anthranilic acid ligands bound to AcpS are described in detail.     

重组蛋白药物的研究进展

近二十几年来蛋白质药物发展迅速。目前有近百种重组蛋白药物上市,几千种处于研发状态。欧美在蛋白质药物研究上整体实力强,在全球有较大的市场。我国重组蛋白药物的研发起步较晚,但发展较快。本文分析了国际和国内蛋白质药物的研发趋势,针对我国基因重组蛋白药物领域现状及存在的问题提出了相应的建议,对国内蛋白质药物研究具有一定的参考价值。