IGIB uses novel drug discovery approach to identify drug targets in TB bacteria


The researchers have already begun finding out novel lead compounds for 15 drug targets.

In a completely different approach to drug discovery, a team led by Dr. Samir K. Brahmachari at Delhi’s CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB) has used a combination of approaches to predict potential drug targets in Mycobacterium tuberculosis, the TB causing bacteria. The novel method not only helps in speeding up drug discovery by finding potential, non-toxic drug targets but will also cost far less by reducing the chances of failure. The results were published in the journal Scientific Reports.

“Conventionally, drug discovery was never looked at from a Systems Biology point of view. The approach we used was rather unconventional. We looked at finding targets first based on evolutionary conservation principle in an organism,” says Dr. Divneet Kaur from IGIB and the first author of the paper. Evolutionary conservation is based on the premise that genes that are very critical for the bacteria do not undergo any mutation.

Based on a previous study that used the Systems Biology Spindle Map (SBSM) approach, the team was able to identify 890 non-toxic genes responsible for metabolism as drug targets. Using computational approaches, the potential drug targets were reduced to 116; these 116 genes are so vital that any inhibition would kill the bacteria.

In order to identify drug targets with the least likelihood of side effects, the 116 essential genes were compared with the human genome and human microbiome at the sequence level to identify genes that did not have any similarity (homology) with human genome sequences.

Of the 116 genes, 104 genes were found to have no similarity with the human genome sequences, meaning any drug developed targeting these 104 genes will only target the TB bacteria and not cause any harm to human cells.

“There is a need for drug discovery to move from Wright brothers’ era of trial and error method. The trial and error approach is slow and too expensive.”The potential drug targets were further shortlisted to 33 genes. The 33 genes play an essential role in bacteria metabolism and have not undergone any mutation in any of the 1,623 TB strains, including the 1,084 multidrug-resistant TB strains, isolated from people with TB. The presence or absence of mutations in any of the 33 genes was evaluated using the Genome-wide Mycobacterium tuberculosis variation (GMTV) database. The genes which are essential for bacteria never undergo any mutations as that would be lethal for their survival.

Potential targets

The crystal structure, which is essential for carrying out drug discovery process, was available for 15 of the 33 targets. “For the 15 genes which have a crystal structure, work has already begun in finding out novel lead compounds for the targets,” says Dr. Mukta Sharma, who is presently involved in the study but is not an author of the paper.

“Once we have the targets and have structures of these targets then can tailor-make molecules to inhibit even MDR-TB and XDR-TB,” says Dr. Kaur. Dr. Debasis Dash from IGIB and one of the authors of the paper helped identify the amino acid changes and mapped them onto the proteins.

The team has already carried out druggability assessment (to find out if the targets have certain properties for a drug to bind to receptors) for all the 33 gene targets. “Most of the 33 genes were found to be highly druggable and none was found to be non-druggable,” says Dr. Sharma. “This validates the approach adopted by this study.”

“There is a need for drug discovery to move from Wright brothers’ era of trial and error method. The trial and error approach is slow and too expensive,” says Dr. Brahmachari. “Through computational approach we first make sure that the target is the Achilles’ heel of M. Tuberculosis and is absent in human cells. Using our new approach, we can work on all organisms.”

According to Dr. Brahmachari, all the genes, targets and even ligands will be in open source so anyone can develop new drug molecules.

Drug resistance

In order to understand the drug resistance seen in many TB drugs, the researchers evaluated the gene targets of known drugs — isoniazid, pyrazinamide, ethambutol for any mutations. “The current drug targets show a high degree of mutations,” says the paper. While isoniazid showed relatively lower variation compared with other drugs, the target of bedaquiline (for MDR-TB) drug showed no mutation. According to the paper, this “supports the hypothesis of the importance of completely invariant genes as potential targets for the successful development of novel antibiotics”.

Metformin, a drug used for diabetes care, was found to have minimum number of mutations, so can be repurposed as an adjunct therapy for MDR-TB.

Published in The Hindu on April 29, 2017

CCMB: Can alpha chain of clusterin protein control weight, fat gain in animals?

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Dr. Ramakrishnan (left), Dr. Mohan Rao (centre) and Suvarsha Matukumalli studied rats injected with beta chain and found fat accumulation from day two onwards.

The two chains of clusterin protein, which are normally expressed in several tissues and can be found in several body fluids, when present together tend to lower lipid levels but administration of one of its chains — alpha or beta — results in completely different outcomes. Cells treated with a recombinant beta chain tend to accumulate fat while cells treated with an alpha chain showed no increase in lipid accumulation. Rabbits administered with a recombinant beta chain showed nearly 40% increase in weight while animals given an alpha chain showed no such increase. The results were published in the journal Scientific Reports.

“Two chains of clusterin when present together tend to decrease body weight but one of the two chains (beta clusterin) increases body weight. This is quite unusual,” says Dr. Ch. Mohan Rao from the Centre for Cellular and Molecular Biology (CCMB), Hyderabad, and the corresponding author of the paper. “So the alpha chain should ideally be compensating for increase in body weight. But the alpha chain does not do that.”

Rats gained lean mass not fat

“While excess energy gets accumulated in the form of fat when beta chain was injected into rats, we did not see this in the case of alpha chain. One possibility is that the alpha chain helps in the metabolism of food in such a way that fat does not accumulate,” he says. “Dissected rats that were given alpha chain showed increased levels of lean mass.”

Apparently, there was no difference in the food intake between animals treated with alpha or beta chain. “It means that weight increase can happen even when there is no increase in food intake. It is the energy management by the body that is important. And alpha chain seems to modulate metabolism in such a way to promote energy expenditure and thus prevent fat accumulation,” he says.

The effect of alpha and beta chains were tested on myoblast cells, fibroblast and cancer cells. The individual chains were injected into rabbits as well. “In my lab we study the effect of small heat shock protein on health and disease. To raise antibody for clusterin we injected the chains separately into rabbits. One set of rabbits was gaining weight while the other did not. That’s when we investigated the reasons. The animal-house in-charge noticed the change in the animals,” recalls Dr. Rao.

Rats too gained weight

Though the effects of the two chains were seen in rabbits, the researchers turned to rats as more animals were required for investigating the effect of individual chains on animals.

“We could see fat accumulation in cells from day two onwards. We observed for 10 days and fat accumulation continued for all the 10 days; we could study cells continuously only for 10 days,” says Suvarsha Rao Matukumalli from CCMB and the first author of the paper. “In the case of animals injected with beta chain, fat accumulation continued for four-five months. The controls and animals given alpha chain did not show weight or fat gain.”

When cells were administered both the chains simultaneously, the cells did not accumulate fat for two-three days but started thereafter. “Fat accumulation was not as much as when only the beta chain was given but fat accumulation nevertheless continued,” says Ms. Matukumalli. But the effect of both the chains in animals was quite different. “When we introduced both alpha and beta chains together in animals we did not see any weight gain. The animals were very much like the controls,” she says. “Only large-scale, in-depth studies can reveal if alpha chain prevents weight gain.”

Published in The Hindu on March 19, 2017

IIT Bombay: Urbanisation has not led to hotter summer days for many Indian cities


The intensity of heat-waves will be lower in the cities compared with non-urban areas as certain cities are not hotter than the surrounding non-urban areas,

Contrary to common notion, a “majority” of 84 cities across India, particularly those in central India and Gangetic Basin, have lower daytime temperature from March to May compared with the surrounding non-urban areas (taken as 1 km radius of the city). Cities with heavily built-up areas and concrete structures are supposed to have higher temperature than non-urban regions due to urban heat island effect.

The results published on January 9 in the journal Scientific Reports based on a 13-year land surface temperature record from satellite sensors is not in agreement with the general understanding of urban climate and surface urban heat island effect in tropical cities. The results once again highlight the importance of increasing the vegetation cover in cities to effectively mitigate the urban heat island effect.

A study by a team of researchers led by Prof. Subimal Ghosh from the Department of Civil Engineering, Indian Institute of technology (IIT) Bombay has shown that while cities have lower daytime temperature than surrounding non-urban areas from March to May, it is the reverse during nights. During night time, the cities, particularly those in the Gangetic Basin, were hotter than non-urban areas.

“This is prominent in cities that are located in the arid region. We didn’t see this in coastal cities as they are not in the arid region,” says Prof. Ghosh, the corresponding author of the paper.

The relatively high vegetation cover leading to higher evapo-transpiration compared with nearby non-urban areas is the main reason why cities are relatively cooler than the adjacent non-urban areas during the day in summer. While the cities have more trees, the non-urban areas are mostly crop lands and are barren during the summer months. The absence of evapo-transpiration during night and the heat contained in the concrete structures increases the night time temperature in the cities during March to May.

Since cities tend to have lower daytime temperature during March to May, the intensity of heat-waves will be lower in the cities compared with non-urban areas. “This is prominent in cities that are located in the arid region. We didn’t see this in coastal cities as they are not in the arid region,” says Prof. Ghosh, the corresponding author of the paper.

During winter (December to February) crops that grow in the non-urban areas result in increased vegetation cover and more evaporative cooling leading lower temperature than in the cities. Also, there is increased biomass burning for cooking and heating in the cities during winter leading to increased emission of black carbon. “The black carbon emission increases the air temperature which may have a feedback to land surface temperature. But this has to be investigated further,” says Prof. Ghosh.

Published in The Hindu on January 9, 2017

IIT Kanpur unravels brown carbon’s effect on atmospheric warming


(From left) Shamjad, Prof. Tripathi and Navaneeth Thamban of IIT Kanpur found brown carbon increases atmospheric warming by absorbing 30 per cent of light

The effect of biomass burning in increasing the atmospheric aerosol and in turn the atmospheric warming through light absorption has been clearly highlighted in a study carried out by a team of researchers from the Indian Institute of Technology (IIT) Kanpur. While the role of black carbon produced by biomass burning in increasing the atmospheric warming has already been well established, the latest study highlights the role of the less known role of brown carbon.

Brown carbon produced by biomass burning has higher light absorption capacity and, therefore, higher capability to increase atmospheric warming. Compared with earlier studies carried out in the U.S, light absorption at 365 nm was found to be five times higher in Kanpur, which has a high biomass burning area. Also, brown carbon accounts for about 30 per cent of light absorption in Kanpur. The results were published on November 24 in the journal Scientific Reports.

“What is seen in Kanpur can be generalised for the entire Indo-Gangetic Plain because the sources of aerosol remain the same throughout the region,” says P.M. Shamjad from the Department of Civil Engineering, IIT Kanpur and the first author of the paper.

“Based on 50 days of measurement (December 23, 2014 to February 24, 2015) we were able to clearly apportion the amount of light absorption by different carbonaceous aerosols. Though brown carbon is 10 times more than black carbon in terms of mass, the absorption capacity of black carbon is 50 times more than brown carbon,” says Prof. S.N. Tripathi from the Department of Civil Engineering, IIT Kanpur and the corresponding author of the paper.

As a result, up to about 70 per cent of light absorption during 24 hours is by black carbon. Brown carbon (when present independently) has nearly 15 per cent potential to warm the atmosphere by absorbing light. Additionally, depending on the spectrum of light, the light absorption capacity of brown carbon is 15-30 per cent when present as a coating (shell) over a black carbon core. “This is because the brown carbon coating behaves like a lens and focuses light towards the black carbon core,” says Shamjad.

The lensing (concentration of light on the core) is dependent on three parameters — ratio of the diameter of the total to the diameter of the core, wavelength of light and the scattering or absorbing property of the coating. “When you have an absorbing coating less light reaches the core. But when the coating is non-absorbent, light gets scattered and more light reaches the core. This leads to more overall light absorption and, in turn, more atmospheric warming,” says Prof. Tripathi.

Unlike at 405 nm (near UV), at 781 nm (near infrared), the lensing becomes predominant as the absorption capacity of the brown carbon coating is non-existent. This is because during daytime, photo bleaching of the brown carbon by sunlight creates a new compound that is no longer able to absorb sunlight.

“The contribution of lensing to light absorption goes up to nearly 35 per cent. This has very serious implications on atmospheric warming,” Prof. Tripathi says.

Published in The Hindu on November 26, 2016

NCBS researchers find a biomarker for stress-induced memory loss


Prof. Sumantra Chattarji (left) and Mohammed Mostafizur Rahman of NCBS, Bengaluru, got some surprising results when they subjected the rats to stress.

Timely intervention to prevent or delay hippocampus-linked memory loss that occurs as a result of chronic stress may now be possible, thanks to the discovery of a biomarker — a reduction in hippocampal volume at an early time point after the onset of chronic stress. The reduction in the hippocampal volume is not only linked to stress-induced memory loss, it may, in fact, be an early risk factor for the eventual development of cognitive impairments. The results were published in the journal Scientific Reports.

A reduction in hippocampal volume and the consequent hippocampus-linked memory loss at the end of chronic stress is already well known both through animal studies and by studying the human brain. “So our question was different. We wanted to study how the diseases progresses and how the damage evolves over time,” says Prof. Sumantra Chattarji from the National Centre for Biological Sciences (NCBS), Bengaluru and one of the authors of the paper.

While all studies in the past have compared the effect of stress on hippocampal volume and memory loss by using two groups of animals (control and experimental group) and studying the effects at the end of the stress period, these researchers took a different approach. They studied the effects in the same animals before and at the end of the study and also at regular intervals during the course of the 10-day stress study in rats.


Rats subjected to stress showed significant reduction in hippocampus volume early on.

Rats react to stress much like humans and hence rats are used as model animals to study the effect of stress on behaviour.

“We undertook a longitudinal study for 10 days and subjected the animals to stress for two hours a day and assessed the animals’ ability to form memories. We got some surprising results,” he says. “At the end of the third day, MRI scans revealed a perceptible and significant reduction in the hippocampus volume. We did not expect to see this within three days.”

The study highlights that rats subjected to stress even for a brief period of three days is sufficient to induce damage to the hippocampus volume. Three days of stress is no where close to being labelled as suffering from chronic stress.

The second major surprise was on the fifth day of the stress. Though MRI scans of the rats on the third day revealed hippocampus volume loss, the rats did not suffer from any hippocampus-linked spatial memory loss even on day five. There was little difference in spatial memory between stressed rats and unstressed rats.

The rats examined at the end of 10 days of stress showed bigger loss of hippocampal volume on the eleventh day and also significant loss of spatial memory on the thirteenth day. “That there was significant loss of memory at the end of 10 days of stress despite no loss on day five was a surprise,” he says.

“We know from earlier work that at the end of stress both hippocampal structure and function are expected to be down. But what we find is that these two go downhill in different ways — structure goes down early and memory loss comes later — but at the end they are both down,” Dr. Chattarji says.

“That means the structural change can act as an early indicator of loss of memory that happens later. The structural deficit precedes the functional or behavioural deficit,” he says. In other words, there is a delayed manifestation of stress-induced impairment of memory loss and the full impact of stress on memory impairment becomes evident at the end of the stress.

The animals that suffered the biggest loss in hippocampal volume on the third day of stress continued to exhibit significant decrease in volume a day after the end of stress. These rats were also the ones that eventually suffered the biggest impairment of spatial memory after the end of stress.

“Right now we don’t know for how long hippocampal volume reduction and memory loss last. Clinical evidence suggests that memory loss persists for an extended period,” says Mohammed Mostafizur Rahman from NCBS and the first author of the paper. “We had earlier shown that dendrites shrink in size and other studies have shown structural changes in cellular morphology.”

Published in The Hindu on November 6, 2016

IISc researchers find a novel, cheaper way to prevent sepsis


IISc researchers – Prof. Dipshikha Chakravortty (left) and Arjun Balakrishnan – used gas nanovesicles produced by Halobacteria to express the cloned BPI gene on its surface to prevent sepsis.

Researchers at the Indian Institute of Science (IISc), Bangalore have demonstrated a cheap and efficacious way of neutralising bacterial endotoxins in blood that cause sepsis. It involves administering a protein into the body of mice. The protein (bactericidal/permeability-increasing protein or BPI) was produced using a novel process. The results were published on September 20 in the journal Scientific Reports.


Sepsis, a life-threatening condition, is triggered by an infection that very quickly spirals out of control and is a major cause for concern among high-risk patients. Sepsis develops when the body mounts a very strong assault on an infection. This results in a cascading effect that causes inflammation in the entire body. It finally ends up as multi-organ failure and death. There is a high mortality rate of 30-50 per cent associated with sepsis.

All the mice treated with BPI survived, while only two mice in the control group did not die.Though the BPI protein, which neutralises the endotoxin that causes sepsis, is produced in the body, sufficient quantities are not produced to quench the endotoxins when sepsis sets in. Therefore, it is necessary to introduce sufficient quantities of BPI protein externally.

Currently, recombinant human BPI, which is used for treating sepsis induced by lipopolysaccharides (LPS), has a few shortcomings — the half-life is short and it is prohibitively expensive.

To address these shortcomings, a team led by Prof. Dipshikha Chakravortty, from the Department of Microbiology and Cell Biology, IISc and the corresponding author of the paper, turned to gas nanovesicles produced by Halobacteria. The nanovesicles are inert in nature and so do not evoke any immune response in humans. Nanovesicles produced by bacteria are easy to purify and so dramatically reduce the production cost of recombinant BPI.

The Bengaluru team along with Prof. Shiladitya DasSarma from the University of Maryland, U.S., cloned mouse BPI protein in the Halobacterium gene so that when the bacteria produced nanovesicles, the BPI protein was expressed on the surface of the vesicles.

“BPI’s stability gets enhanced when expressed on the surface of the nanovesicles probably because it is anchored to the nanovesicle membrane,” says Prof. Chakravortty. The mouse BPI expressed on the surface of nanovesicles showed antibacterial activity.

To test the efficacy of BPI expressing nanovesicles from preventing sepsis, the 50 mice were first injected with nanovesicles and then challenged with sepsis causing LPS and galactosamine. “All the mice treated with BPI survived, while only two mice in the control group did not die,” says Arjun Balakrishnan, the first author of the paper.

However, when BPI expressing nanovesicles were administered along with or after sepsis causing LPS treatment the mice did not survive. “This suggests that BPI proteins should be administered before sepsis sets in so that it is present in the circulatory system to clear the sepsis-causing endotoxin,” says Prof. Chakravortty. “Cytokine storm will set in within minutes of septic shock. So nothing can be done once sepsis sets in.”

“The therapeutic use of BPI produced in Halobacterium to combat septic shock may be promising from the standpoint of both safety and efficacy,” says Mr. Balakrishnan. The team is now planning to undertake trials in larger animals.

Published in The Hindu on September 25, 2016 

IIT Bombay: Extreme rainfall not associated with warming

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The researchers did not find evidence to support the notion that intensification in either the mean or extreme rainfall over India was due to warming.

A study carried out by researchers at IIT Bombay has found that extreme rainfall events over India do not have significant association with land surface air temperature over India and sea surface temperature over central Indian Ocean.

The results are contrary to the general notion that global warming or increased summer temperature is responsible for extreme summer monsoon rainfall events witnessed in some parts of India in the last few years. The results are applicable at both large and small scales — Indian subcontinent and at a grid level of 100 x 100 sq. km. Data for 50 years pre- and post-1975s were used for the study. The results are published today (August 3, 2016) in the journal Scientific Reports.

In the recent past, there has been considerable change in heavy summer monsoon rainfall pattern in India and there is considerable debate on whether such extreme events are caused by global warming or by urbanisation.

A December 2006 paper in Science by B.N. Goswami of the Indian Institute of Tropical Meteorology, Pune, attributed the increase in magnitude and frequency of heavy rainfall events over central India to global warming. But Goswami used a spatial average over central India, a convenient way to carry out the analysis but unfortunately missed some of the spatial details and overstated some of the conclusions. But the latest study found insignificant dependence of precipitation extreme on temperature over India.

At a local level, some of the grids of 100×100 sq. km. experienced a change in extreme rainfall with increasing temperature, while other grids witnessed a decrease or no significant change in rainfall with increased temperature. The model simulation of Indian rainfall extremes tends to “overestimate the changes in both mean and extreme precipitation”.

The study also found that dynamic moisture transport caused by thermal gradient between land and water had a significant role on mean and extreme rainfall compared with direct thermodynamic effect (where the atmosphere has a greater capacity to carry moisture when temperature rises).  “The dynamic transfer into the subcontinent is associated with thermodynamic processes in the nonlocal regions involved — it is the competition for rain over India versus over the ocean,” Prof. Raghu Murtugudde a co-author from the University of Maryland, Maryland, U.S. explains in an email to me.

The new generation climate model and historical simulations tend to over-estimate the association between extreme rainfall events and temperature.On a global scale, increase in rainfall extremes in a warming world is generally explained by the Clausius-Clapeyron equation.  The C-C equation states that with an increase in temperature the precipitation too increases as the moisture-carrying capacity of air increases with temperature (at a rate of 7.5 per cent per degree increase in temperature). But the C-C scaling will not be applicable in many of the tropical regions.

A study carried out in Brazil revealed that there was a decrease in extreme rainfall with increasing temperature. In the latest study too, the researchers did not find evidence to support “intensification in either the mean or extreme rainfall over India in a warming world”.

“The claim is not really that climate change is not important. But the novel results indicate that the local warming is not the controlling factor. The clues are in the rapid warming of the Indian Ocean and the changing roles of the Arabian Sea, Bay of Bengal and the Indian Ocean in monsoon variability and extremes. It is the nonlocal controls that are of great importance,” says Prof. Murtugudde.

“The new generation climate model and historical simulations tend to over-estimate the association between extreme rainfall events and temperature. We must be careful while using climate change for estimating future changes in extreme rainfall with increasing temperature over India and Central Indian Ocean,” says Prof. Subhankar Karmakar a co-author of the paper from the Centre for Environmental Science and Engineering, IIT Bombay.

“The changing patterns of extremes over the Indian subcontinent need a scientific re-evaluation.  Our results highlight the need for further research to resolve the temperature dependence of rainfall,” says Prof. Subimal Ghosh, a co-author of the paper from the Department of Civil Engineering, IIT Bombay.

Published in The Hindu on August 3, 2016