Current Medicinal Chemistry - Volume 16, Issue 3, 2009

High-throughput screening campaigns are fuelled not only by corporate or “maximally diverse” compound collections, but increasingly accompanied by target- or bioactivity-focused selections of screening compounds. Computerassisted library design methods aid in the compilation of focused molecule libraries. A prerequisite for application of any such computational approach is the definition of a reference set and a molecular similarity metric, based on which compound clustering and iterative virtual screening are performed. In this context the self-organizing map (SOM, Kohonen network) and variations thereof have found widespread application. SOMs cover such diverse fields of drug discovery as screening library design, scaffold-hopping, and repurposing. Here we present the concept of the SOM technique along with recent case studies. Advantages, limitations and potential future applications are critically discussed.

The Human Immunodeficiency Virus (HIV) genome encodes three major structural proteins common to all retroviruses (Gag, Pol and Env), two regulatory proteins (Tat and Rev) that are essential for viral replication, and four accessory proteins (Nef, Vif, Vpu, Vpr). While accessory proteins were initially reported to be unnecessary for viral growth, their importance as virulence factors is now being more and more appreciated: they can dramatically alter the course and severity of viral infection, replication and disease progression. None of the HIV accessory proteins display enzymatic activity: they rather act altering cellular pathways via multiple protein-protein interactions with a number of host cell factors. All currently approved anti-HIV drugs target pol and env encoded proteins. Therefore, widening the molecular targets of HIV therapy by additionally targeting accessory proteins may expand treatment options, resulting in high impact effective new therapy. In this review we present the state of the art of compounds that target HIV accessory proteins. Most of the research has focused on the inhibition of specific accessory proteins/host cell partner interactions. Promising compounds have been found within different classes of molecules: small natural and synthetic molecules, peptides and proteins, oligonucleotides, in particular those used as RNA interference (RNAi) tools. With the assortment of compounds available, especially against Nef and Vif functions, the demonstration of the clinical efficacy of the new anti-HIV-1 drugs targeting accessory proteins is next challenge.

Anticancer drug-induced tumor suppression may involve mechanisms of protection against neoplastic transformation that are normally latent in mammalian cells and consist in a genetic program implemented during anti-tumoral defense. This defense program results in the self elimination of cells harboring potentially dangerous mutations by triggering cell death through apoptosis and/or autophagy or in the execution of a program that leads to a permanent growth arrest known as senescence. These responses are considered crucial tumor suppressive mechanisms and their study appears to be essential to develop therapeutical procedures based on the enhancement of the different responses. This review summarizes fundamental knowledge on the underlying mechanisms able to limit excessive or aberrant cellular proliferation and on the prognostic value of both apoptosis and senescence detection. In addition, interesting evidence showing that different drugs induce senescence or cell death depending on the genetic features of the tumor cells as well as on the integrity of the relative pathways is reported.

Chemoresistance is a general health problem concerning infectious diseases and cancer treatments. In this context, the worldwide dissemination of ≪ pandrug ≫ and ≪ multidrug≫ resistant pathogens has severely compromised the efficacy of our antimicrobial weapons and dramatically increased the occurence of therapeutic failure. To efficiently combat multi-resistant pathogens, it is necessary to clearly define the molecular basis of the general resistance mechanism associated with the expression of active efflux pumps, which strongly restrict the intracellular concentration of antimicrobial drugs. Several families of efflux systems capable of multiple drug extrusion have been described. The activity of some efflux systems requires ATP hydrolysis for drug transport while others require a sodium or proton antiport. In this review we focus on two important human pathogens, Plasmodium falciparum and Pseudomonas aeruginosa, which exhibit a high level of antimicrobial resistance associated with the expression of efflux mechanisms. The efflux mechanisms and the development of efflux pump inhibitors (EPIs) are discussed regarding these two pathogens.

Fourier-transform infrared (FT-IR) based mapping and imaging is a fast emerging technology which is being increasingly applied to investigate tissues in the high-throughput mode. The high resolution close to the cellular level, the possibility to determine the bio-distribution of molecules of interest (proteins, peptides, lipids, carbohydrates) without any pre-treatment and the offer to yield molecular structure information have brought evidence that this technique allows to gain new insights in cancer pathology. Thus, several individual mainly protein and peptide cancer markers (“biomarkers”) can be identified from FT-IR tissue images, enabling accurate discrimination between healthy and tumour areas. Optimal data acquisition (spatial resolution, spectral resolution, signal to noise ratio), classification, and validation are necessary to establish practical protocols that can be translated to the qualitative and quantitative clinical routine analysis. Thereby, the development of modern fast infrared imaging systems has strongly supported its acceptance in clinical histopathology. In this review, the necessity of analysis based on global cancer statistics, instrumental setups and developments, experimental state of the art are summarised and applications to investigate different kinds of cancer (e.g., prostate, breast, cervical, colon, oral cavity) are shown and discussed in detail.

Podophyllotoxin is an important and much sought after antimitotic natural lead compound, since it paved the way for three hemisynthetic derivatives of podophyllotoxin, e.g., etoposide, teniposide and etopophos, which are widely used as anticancer drugs and show good clinical effects against several types of neoplasms. Although the publication of the recent reviews by Gordaliza in 2004 and You in 2005, which covered the literatures concerning podophyllotoxin until the early part of 2003, there have been significant number of works carried out on podophyllotoxin recently. Therefore, this review presents up-to-date coverage of podophyllotoxin in regard to hemisynthesis, biosynthesis, biological activities, mode of action and structure-activity relationship.

Long term caloric restriction is known to counteract aging and extend lifespan in several organisms from yeasts to mammals. Recent research has provided solid ground to the concept that limiting calorie intake slows down brain aging and protects from age-related neurodegenerative diseases. The present review summarizes the most relevant among these data and highlights some genetic and molecular mechanisms responsible for caloric restriction-related neuroprotection. To understand these mechanisms is important because this information makes them potential targets for therapeutic intervention aimed at reproducing the metabolic, genetic and molecular features responsible for the beneficial effect of caloric restriction. Most promising among these targets are neurotrophins, such as BDNF, transcription factors, such as FoxO and PPAR, anti-aging proteins, such as sirtuins, and caloric restriction mimetics acting on oxidative stress and energy metabolism. Notwithstanding the complexity of any therapeutic strategy aimed at reproducing the beneficial effects of caloric restriction, due to multiplicity of the cellular pathways involved in the responses, a great expansion of medicinal chemistry research in this field is expected in the next future.

Proteins almost never act in an isolated manner; they interact with other proteins in order to perform essential roles in many important cellular processes. Apart from their ability to form stable multiprotein complexes, proteins associate transiently with their targets to modify, regulate by steric effects, or translocate them to different cellular compartments. Therefore, the identification of molecules able to modulate such protein contacts is of significant interest for drug discovery and chemical biology, since it provides a means to exert control over cellular events. Nevertheless, finding antagonists of protein interactions displaying both target affinity and selectivity in the complex context of the cell proteome is a challenging task, because of the generally large, noncontiguous, interfaces involved in protein interactions. In this review we focus on recent advances in the detection, analysis and specific interference of protein interactions. These studies provide the basis for a promising avenue in medicinal chemistry towards the selective regulation of biochemical pathways.

Prion diseases are zoonotic infectious diseases caused by infectious particles, termed prions. Main component of prions is presumably a misfolded, partially protease-resistant conformer (PrPSc) of a normal cell surface protein, the cellular prion protein (PrPC), whose anti-oxidative role is presumed by studies using prion protein (PrP)-knockout mice and cell lines. Major common features of prion diseases are PrPSc deposition, astrocytosis, and vacuolation, but the presence of these features and transmission route are dependent on the combination of prion strain and host species. Generally, prions replicate first in the lymphoreticular system, although the presence of PrPSc within lymphoid tissues seems to be dependent on factors such as route of prion exposure or type of prion strain. After that, prions travel to the brain via neuronal pathways along peripheral nerves, where their conversion leads to the accumulation of PrPSc and a deficiency of PrPC, contributing etiologically to the death of neurons including apoptosis and autophagy. In this review, we provide an overview of current information on PrPC and PrPSc as well as their involvement in the pathogenesis of prion diseases.

Ensuring the availability of new antibiotics to eradicate resistant pathogens is a critical issue, but very few new antibacterials have been recently commercialized. In an effort to rationalize their discovery process, the industry has utilized chemical library and high-throughput approaches already applied in other therapeutical areas to generate new antibiotics. This strategy has turned out to be poorly adapted to the reality of antibacterial discovery. Commercial chemical libraries contain molecules with specific molecular properties, and unfortunately systemic antibacterials are more hydrophilic and have more complex structures. These factors are critical, since hydrophobic antibiotics are generally inactive in the presence of serum. Here, we review how the skewed distribution of systemic antibiotics in chemical space influences the discovery process.