Jayakanthan Mannu

A computational study of CYP3A4 mediated drug interaction profiles for anti-HIV drugs

AbstractMolecular docking is a reliable method with which to identify the binding conformations of substrates, inducers and inhibitors of cytochrome P450 (CYP) enzymes. We used the docking method to explore possible binding modes of an entry inhibitor (maraviroc) and non-nucleoside reverse transcriptase inhibitors (delavirdine, efavirenz and etravirine) to cytochrome P450 3A4 (CYP3A4). In addition, docking results were compared with the binding conformations of HIV protease drugs to infer the binding site residues and potential drug–drug interaction profiles for combination therapy in the treatment of AIDS. We observed that efavirenz and etravirine induce metabolism of co-administered drugs by binding to a unique position in the active site of CYP3A4. Dosage adjustment is required for delavirdine and maraviroc when combined with HIV protease drugs. The present results are in good agreement with experimental data from drug interaction profiles. The information provided in this paper will be helpful in furthering our understanding the functions of CYP3A4, and could aid in the design of new drugs that would be metabolized easily without having any drug–drug interaction profile. FigureThe docked poses of etravirine (ETR) inside the active site of cytochrome P450 3A4 (CYP3A4). The binding site residues are colored by atom type: gray carbon, red oxygen, blue nitrogen, cyan hydrogen, yellow sulfur. The sticks of the ligands and heme are colored in green.

Interactions of laminin β3 fragment with β1-integrin receptor: A revisit of the apical ectoplasmic specialization-blood-testis-barrier-hemidesmosome functional axis in the testis

Recent studies have demonstrated the presence of a functional axis that coordinates the events of spermiation and blood-testis barrier (BTB) restructuring which take place simultaneously at opposite ends of the seminiferous epithelium at stage VIII of the epithelial cycle of spermatogenesis in the rat testis. In short, the disruption of the apical ectoplasmic specialization (apical ES) at the Sertoli cell-elongated spermatid interface, which facilitates the release of sperm at spermiation near the tubule lumen, is coordinated with restructuring at the BTB to accommodate the transit of preleptotene spermatocytes near the basement membrane. These two events are likely coordinated by a functional axis involving hemidesmosome at the Sertoli cell-basement membrane interface, and it was designated the apical ES-BTB-hemidesmosome axis. It was demonstrated that fragments of laminin chains (e.g., laminin β3 or γ3 chains) derived from the α6β1-integrin-laminin333 protein complex at the apical ES, which were generated via the action of MMP-2 (matrix metalloprotease-2, MMP2) prior to spermiation, acted as biologically active peptides to perturb the BTB permeability function by accelerating protein endocytosis (e.g., occludin) at the site, thereby destabilizing the BTB integrity to facilitate the transit of preleptotene spermatocytes. These laminin fragments also perturbed hemidesmosome function via their action on β1-integrin, a component of hemidesmosome in the testis, which in turn, sent a signal to further destabilize the BTB function. As such, the events of spermiation and BTB restructuring are coordinated via this functional axis. Recent studies using animal models treated with toxicants, such as mono-(2-ethylhexyl) phthalate (MEHP), or adjudin, a male contraceptive under investigation, have also supported the presence of this functional axis in the mouse. In this short review, we critically evaluate the role of this local functional axis in the seminiferous epithelium in spermatogenesis. We also provide molecular modeling information on the interactions between biologically active laminin fragments and β1-integrin, which will be important to assist in the design of more potent laminin-based peptides to disrupt this axis, thereby perturbing spermatogenesis for male contraception and to understand the underlying biology that coordinates spermiation and BTB restructuring during spermatogenesis.

The apical ectoplasmic specialization-blood-testis barrier functional axis is a novel target for male contraception.

The blood-testis barrier (BTB), similar to other blood-tissue barriers, such as the blood-brain barrier and the blood-retinal barrier, is used to protect the corresponding organ from harmful substances (e.g., xenobiotics) including drugs and foreign compounds. More importantly, the BTB allows postmeiotic spermatid development to take place in an immune privileged site at the adluminal (or apical) compartment to avoid the production of antibodies against spermatid-specific antigens, many of which express transiently during spermiogenesis and spermiation. The BTB, however, also poses an obstacle in developing nonhormonal-based male contraceptives by sequestering drugs (e.g., adjudin) that exert their effects on germ cells in the adluminal compartment. The effects of these drugs include disruption of germ cell cycle progression and development, apoptosis, cell adhesion, metabolism and others. Recent studies have demonstrated that there is a functional axis that operates locally in the seminiferous epithelium to co-ordinate different cellular events across the Sertoli cell epithelium, such as spermiation and BTB restructuring during the seminiferous epithelial cycle of spermatogenesis. Components of this functional axis, such as the apical ectoplasmic specialization (apical ES, a testis-specific atypical anchoring junction type) and the BTB, in particular their constituent protein complexes, such as alpha6beta1-integrin and occludin at the apical ES and the BTB, respectively, can be the target of male contraception. In this chapter, we highlight recent advances regarding the likely mechanism of action of adjudin in this functional axis with emphasis on the use of molecular modeling technique to facilitate the design of better compounds in male contraceptive development.

Computational analysis of CYP3A4-mediated metabolism to investigate drug interactions between anti-TB and anti-HIV drugs in HIV/TB co-infection

The treatment of human immunodeficiency virus (HIV)-related tuberculosis (TB) includes combination therapy, in which antiretroviral drugs and anti-TB drugs are co-administered. The complexities associated with the treatment of dual infection by Mycobacterium tuberculosis and HIV include occurrence of drug–drug interactions, in addition to pill burden, overlapping drug toxicity, and immune reconstitution inflammatory syndrome. Drug–drug interactions can occur between these drugs toward cytochrome P450 3A4 (CYP3A4), a drug-metabolizing enzyme. A thorough understanding of these interactions can prevent occurrence of treatment failures and drug toxicity. Molecular docking studies were carried out for FDA-approved drugs, to predict binding mechanism of anti-TB drugs with CYP3A4 and to compare them with our previous studies on antiretroviral drugs, in order to infer possible occurrence of drug–drug interactions. The core regimen of anti-TB treatment viz., rifampin (RIF), isoniazid (INH), and pyrazinamide (PZA) showed similar binding mode (i.e., competitive binding) via utilizing the same binding residue, Arg212 in CYP3A4. This regimen also shared similar binding mode with antiretroviral protease inhibitors except tipranavir, nelfinavir, lopinavir, and atazanavir. Contraindicated drug interactions were not observed between non-nucleoside reverse transcriptase inhibitors, delavirdine, efavirenz, and etravirine; and anti-TB drugs, RIF, INH, and PZA. The contraindications occurring within anti-TB drugs can be negated with inhibitory effect of INH to induction effect of RIF toward CYP3A4. We evaluated the importance of Arg212 along with Ser119, Ala370, Arg372, and heme moiety for mediating oxidative metabolism of drugs. These drug interaction details were incorporated into our web server by creating a database called “CYP3A4 DDIDB” and it is open accessible from http://cyp.bicpu.edu.in.

Role of Bioinformatics in Drug Resistance Prediction for HIV/AIDS

The successful treatment of human immunodeficiency virus (HIV) infection is majorly affected by development of viral drug resistance. This complicates physician to choose the right choice of drugs. In such a scenario, a series of bioinformatics software tools and databases have been developed for predicting drug resistance, and responses to combination therapy from viral genotype have been developed to support physician. In this paper, we provided an up-to-date review on current treatment options, exploring the potential of novel targets and developed computational tools and databases for current HIV therapy in viral drug resistance.

In Silico Approach to Identify Potential Inhibitors for Axl-Gas6 Signaling

Axl-Gas6 signaling plays an important role in numerous cancers. Axl kinase, a member of receptor tyrosine kinase family is activated by different mechanisms with Gas6 as its major activator. Targeting the Axl with inhibitors may block the binding of Gas6 and further hinders the activation of Axl. This in turn inhibits the Axl-Gas6 signaling. Thus, inhibitors of the Axl kinase may serve as ideal drug candidates for treating many human cancers. In this study we carried out virtual screening of drug-like molecules from ZINC database to identify potential inhibitors for Axl kinase. Our virtual screening study showed that ZINC83758120, ZINC34079369, and ZINC83758121 are potential drug-like lead molecules to inhibit Axl kinase.

Nonreceptor Protein Kinases c-Src, c-Yes, and FAK Are Biomarkers for Male Contraceptive Research

A major obstacle in male contraceptive research and development is the lack of reliable and sensitive biomarkers to monitor the efficacy and potency of candidate compounds under investigation. Since the use of routine andrology techniques/analyses, such as sperm count, sperm motility, sperm morphology, sperm DNA integrity, sperm metabolism, and other semen characteristics (e.g., semen volume, pH, bacterial content) are tedious, representing the combined changes that take place in the testis and the male reproductive tract including the epididymis, rete testis, efferent ducts, prostate, and seminal vesicles. As such, the number of compounds that can be rapidly screened and tested is severely limited. Also, the outcomes are often difficult to interpret since it is not known if a compound under investigation exerts its effects mostly in the testis, the epididymis, another accessory sex organ or a combination of these organs. Herein, we summarize recent findings in the field regarding the use of nonreceptor protein kinases c-Src, c-Yes, and FAK as possible biomarkers for male contraceptive development based on our experience with adjudin, 1-(2,4-dichlorobenzyl)-1H-indazole-3-carbohydrazide (formerly known as AF-2364). This information should pave the way of using these, and possibly other, markers for male contraceptive research.