Toward novel HIV-1 integrase binding inhibitors: Molecular modeling, synthesis, and biological studies

Iron-Catalyzed Oxidative Decarbonylative α-Alkylation of Acyl-Substituted Furans with Aliphatic Aldehydes as the Alkylating Agents

A protocol for FeCl₂-catalyzed oxidative decarbonylative α-alkylation of acyl furans using alkyl aldehydes as the alkylating agents has been developed. This protocol affords α-alkyl-α-acylfurans in moderate to good yields in a practical and sustainable fashion. Mechanistic studies suggest that the reaction proceeds via generation of an alkyl radical from the alkyl aldehyde, addition of the radical to the furan ring, and subsequent rearomatization.

Simple Chemoinformatics Criterion Using Electron Donor-Acceptor Molecular Characteristics for Selection of Antibiotics Against Multi-Drug-Resistant Bacteria

Recent outbreaks of NDM-1-positive Entero-bacteriaceae in Great Britain and India and the highly pathogenic Escherichia coli strain EHEC O104:H4 in Germany and some other E.U. countries point out an urgent need for the ability to decide on appropriate antibiotics to treat multi-drug-resistant (MDR) bacteria. Here we propose a simple criterion for choosing antibiotics based on characteristics of electron donor and acceptor properties. Using molecular descriptors, such as electron-ion interaction potential (EIIP) and average quasi-valence number (AQVN), which can describe potential long-range interactions between therapeutic molecules and their targets, we have been able to suggest appropriate antibiotics for treatment of MDR bacterial infections. To demonstrate the prospective usefulness of these molecular descriptors we have used this informatics system to propose that pleuromutilins and nitrofurans could be effective against of NDM-1-positive Enterobacteriacea and that aminoglycosides, macrolides and pluromutilins (and possibly nitrofurans) could be suitable for treatment of the highly pathogenic Escherichia coli strain EHEC O104:H4. Similarly, because of their specific electronic properties, we can also suggest antibiotics that could be potentially effective against other MDR bacteria. The proposed antibiotics should be further evaluated for their treatment potentials.

Comprehensive Review in Current Developments of Benzimidazole-Based Medicinal Chemistry

The properties of benzimidazole and its derivatives have been studied over more than one hundred years. Benzimidazole derivatives are useful intermediates/subunits for the development of molecules of pharmaceutical or biological interest. Substituted benzimidazole derivatives have found applications in diverse therapeutic areas such as antiulcer, anticancer agents, and anthelmintic species to name just a few. This work systematically gives a comprehensive review in current developments of benzimidazole-based compounds in the whole range of medicinal chemistry as anticancer, antibacterial, antifungal, anti-inflammatory, analgesic agents, anti-HIV, antioxidant, anticonvulsant, antitubercular, antidiabetic, antileishmanial, antihistaminic, antimalarial agents, and other medicinal agents. This review will further be helpful for the researcher on the basis of substitution pattern around the nucleus with an aim to help medicinal chemists for developing an SAR on benzimidazole drugs/compounds.

Computational methods in drug discovery

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature.

Synthesis and biological evaluation of nitromethylene neonicotinoids based on the enhanced conjugation

The neonicotinoids with a nitroconjugated system had excellent bioactivity, which could rival imidacloprid, and has been previously reported. However, the photodegradation and hydrolysis of this series of neonicotinoids was very quick according to our further investigation, which cannot be developed as a pesticide further. The approach to further enhance the conjugation was tried not only to increase the bioactivities but also to improve the stability in water and in the sun. A substituted phenyl group was introduced into the furan ring of compound 3. A total of 13 novel neonicotinoid analogues with a higher conjugation system were designed and synthesized. The target molecular structures have been confirmed on the basis of satisfactory analytical and spectral data. All compounds presented significant insecticidal activities on cowpea aphid ( Aphis craccivora ), cotton aphid ( Aphis gossypii ), and brown planthopper ( Nilaparvata lugens ). The stability test exhibited that the stability of novel analogues in water and under the mercury lamp has been improved significantly in comparison to compound 3.

New in silico and conventional in vitro approaches to advance HIV drug discovery and design

INTRODUCTION

Recently, the new concept of the long-range intermolecular interactions in biological systems has been proposed. Combined use of molecular modeling techniques and the screening techniques based on the long-range interaction concept could significantly improve and accelerate discovery of new HIV drugs. However, any hit identified in silico needs to be characterized with respect to its biological target by enzymatic studies. Combined use of the in silico screening and the enzymatic studies allows an efficient selection of new anti-HIV drugs.

AREAS COVERED

The focus of this article is on the in silico screening of molecular libraries for candidate new HIV drugs, which is based on the molecular descriptors determining the long-range interaction between the drugs and their therapeutic target. This article also reviews the techniques for enzyme kinetic studies which are required for optimization of in silico selected candidate anti-HIV drugs.

EXPERT OPINION

The novel approach of combining in silico screening techniques with enzymatic studies enables the accurate measurement of the quantitative descriptors of ligand-enzyme interactions. This novel method is a powerful tool for new anti-HIV drug discovery which can also reduce the drug development costs.

The role of long-range intermolecular interactions in discovery of new drugs

INTRODUCTION

Long-range intermolecular interactions (interactions at distances between 100 and 1000 Å) play an important role in the interaction between drugs and therapeutic targets, and design techniques based on this concept could significantly improve and accelerate new drug discovery. Understanding these long-range intermolecular interactions will also help further our understanding of the molecular mechanisms and the underlying basic biological processes.

AREAS COVERED

This article looks at the physical bases of long-range intermolecular interactions in biological systems with a brief review of the literature data to support this concept. The article also gives some examples of techniques used in drug discovery that were based on the long-range intermolecular interaction concept.

EXPERT OPINION

The electron-ion interaction potential (EIIP) and average quasivalence number (AQVN) concepts shed new light on the role of long-range intermolecular interactions in biological systems. Further research of physicochemical mechanisms underlying long-range interactions between biological molecules is necessary for a better understanding of the basic biological processes. The addition of the computer-aided design techniques based on the EIIP/AQVN concept to the research and development will lead not only to a significant reduction in cost but also to an acceleration in the development of new drugs.

A versatile and practical synthesis toward the development of novel HIV-1 integrase inhibitors

As a continuation of our previous work, which resulted in the identification of a new hit compound as an HIV-1 integrase inhibitor, three novel series of salicylic acid derivatives were synthesized using three versatile and practical synthetic strategies and were assayed for their capacity to inhibit the catalytic activity of HIV-1 integrase. Biological evaluations revealed that some of the synthesized compounds possess good inhibitory potency in enzymatic assays and are able to inhibit viral replication in MT-4 cells at low micromolar concentrations. Finally, docking studies were conducted to analyze the binding mode of the synthesized compounds within the DNA binding site of integrase in order to refine their structure-activity relationships.

Molecular dynamics and DFT study on HIV-1 nucleocapsid protein-7 in complex with viral genome

The HIV-1 nucleocapsid protein-7 (NCp7) is a highly basic, small zinc-binding protein involved in both deoxyribonucleic (DNA) and ribonucleic (RNA) acids annealing and in viral particle maturation including genome encapsidation, with an additional chaperoning activity toward reverse transcriptase by promoting the two obligatory strand transfers during reverse transcription. Because of its interaction with highly conserved sequences of the HIV-1 genome, NCp7 is being considered a new potential drug target, resistant to mutation, for antiviral activity. The high flexibility of this protein has, however, limited the identification of structural determinants involved in the interaction with stranded sequences of DNA and RNA. Here, we provide a quantum mechanics (density functional theory) study of the zinc-binding motifs and a molecular dynamics simulation of the protein in complex with RNA and DNA, starting from available nuclear magnetic resonance (NMR) structures. Results show that the interaction between the NCp7 and the viral genome is probably based on electrostatic interactions due to a cluster of basic residues, which is reinforced by the exploitation of nonelectrostatic contacts that further stabilize the complexes. Moreover, a possible mechanism for DNA destabilization that involves amino acids T24 and R26 is also hypothesized. Finally, a network of hydrophobic and hydrogen-bond interactions for the stabilization of complexes with DNA and, especially, with RNA is described here for the first time. The complexes between NCp7 and both DNA and RNA, resulting from computer simulations, showed structural properties that are in agreement with most of the currently available molecular biology evidence and could be considered as reliable models (better than NMR structures currently available) for subsequent structure-based ligand design approaches.

Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection

The HIV replication cycle offers multiple targets for chemotherapeutic intervention, including the viral exterior envelope glycoprotein, gp120; viral co-receptors CXCR4 and CCR5; transmembrane glycoprotein, gp41; integrase; reverse transcriptase; protease and so on. Most currently used anti-HIV drugs are reverse transcriptase inhibitors or protease inhibitors. The expanding application of simulation to drug design combined with experimental techniques have developed a large amount of novel inhibitors that interact specifically with targets besides transcriptase and protease. This review presents details of the anti-HIV inhibitors discovered with computer-aided approaches and provides an overview of the recent five-year achievements in the treatment of HIV infection and the application of computational methods to current drug design.

Exploration of novel thiobarbituric acid-, rhodanine- and thiohydantoin-based HIV-1 integrase inhibitors

A novel compound inhibiting HIV-1 integrase has been identified by means of virtual screening techniques. A small family of structurally related molecules has been synthesized and biologically evaluated with some of the compounds possessing micromolar activity both in enzymatic and cellular assays.